Starting phenix.real_space_refine on Thu Mar 5 21:44:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7p_31777/03_2026/7v7p_31777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7p_31777/03_2026/7v7p_31777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7p_31777/03_2026/7v7p_31777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7p_31777/03_2026/7v7p_31777.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7p_31777/03_2026/7v7p_31777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7p_31777/03_2026/7v7p_31777.cif" } resolution = 2.9 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= -0.002 sd= 0.039 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 108 5.16 5 C 16114 2.51 5 N 4129 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25371 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.40, per 1000 atoms: 0.25 Number of scatterers: 25371 At special positions: 0 Unit cell: (143, 145.2, 199.1, 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 108 16.00 O 5020 8.00 N 4129 7.00 C 16114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.04 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.02 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 341 " " NAG J 1 " - " ASN A 614 " " NAG K 1 " - " ASN A 707 " " NAG L 1 " - " ASN A 715 " " NAG M 1 " - " ASN A 799 " " NAG N 1 " - " ASN A1072 " " NAG O 1 " - " ASN A1096 " " NAG P 1 " - " ASN A1132 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 163 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 44 sheets defined 25.1% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.243A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 4.026A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.755A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 896 through 906 removed outlier: 3.596A pdb=" N TYR A 902 " --> pdb=" O MET A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.300A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.594A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.749A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.705A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.126A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.557A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.567A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.806A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.634A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.696A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.066A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.727A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.633A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.315A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.508A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.771A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 4.488A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.951A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.913A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.653A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 916 removed outlier: 4.382A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 910 through 916' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 3.646A pdb=" N ALA C 987 " --> pdb=" O ASP C 983 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.861A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.464A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.416A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.114A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.559A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.454A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.757A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.013A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.679A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.541A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.508A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.966A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.086A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.195A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.430A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.491A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC5, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.350A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC7, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.965A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 699 through 702 removed outlier: 7.006A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LYS C 788 " --> pdb=" O ALA B 699 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN B 701 " --> pdb=" O LYS C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.023A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.516A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1074 through 1076 removed outlier: 4.048A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD5, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.876A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.054A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.629A pdb=" N GLY C 103 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.137A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE1, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.821A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE3, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE4, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.043A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.812A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C1057 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.470A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 1005 hydrogen bonds defined for protein. 2733 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7992 1.34 - 1.46: 6251 1.46 - 1.58: 11547 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25922 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.24e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C PRO C 984 " pdb=" N PRO C 985 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.34e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 25917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 35243 4.89 - 9.78: 29 9.78 - 14.68: 0 14.68 - 19.57: 0 19.57 - 24.46: 1 Bond angle restraints: 35273 Sorted by residual: angle pdb=" C LEU A 982 " pdb=" N ASP A 983 " pdb=" CA ASP A 983 " ideal model delta sigma weight residual 120.49 144.95 -24.46 1.42e+00 4.96e-01 2.97e+02 angle pdb=" N ILE A 803 " pdb=" CA ILE A 803 " pdb=" C ILE A 803 " ideal model delta sigma weight residual 113.53 109.75 3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.50 -3.80 1.22e+00 6.72e-01 9.73e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.82 -6.35 2.06e+00 2.36e-01 9.49e+00 angle pdb=" N PRO C 984 " pdb=" CA PRO C 984 " pdb=" C PRO C 984 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.48e+00 ... (remaining 35268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 14894 17.73 - 35.46: 1276 35.46 - 53.20: 281 53.20 - 70.93: 67 70.93 - 88.66: 31 Dihedral angle restraints: 16549 sinusoidal: 7537 harmonic: 9012 Sorted by residual: dihedral pdb=" CB CYS C1080 " pdb=" SG CYS C1080 " pdb=" SG CYS C1124 " pdb=" CB CYS C1124 " ideal model delta sinusoidal sigma weight residual -86.00 1.97 -87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS B 536 " pdb=" SG CYS B 536 " pdb=" SG CYS B 588 " pdb=" CB CYS B 588 " ideal model delta sinusoidal sigma weight residual -86.00 -7.43 -78.57 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -163.24 77.24 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 16546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3670 0.071 - 0.142: 562 0.142 - 0.213: 15 0.213 - 0.284: 2 0.284 - 0.355: 1 Chirality restraints: 4250 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 601 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 601 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4247 not shown) Planarity restraints: 4504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 984 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO C 984 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1054 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO C1055 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C1055 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C1055 " 0.025 5.00e-02 4.00e+02 ... (remaining 4501 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1514 2.73 - 3.27: 24634 3.27 - 3.82: 39386 3.82 - 4.36: 45247 4.36 - 4.90: 81020 Nonbonded interactions: 191801 Sorted by model distance: nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP C 566 " pdb=" OG1 THR C 570 " model vdw 2.222 3.040 nonbonded pdb=" O ASN A 437 " pdb=" OG SER A 441 " model vdw 2.227 3.040 ... (remaining 191796 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' selection = (chain 'B' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' 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 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.790 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26046 Z= 0.186 Angle : 0.637 24.459 35605 Z= 0.316 Chirality : 0.047 0.355 4250 Planarity : 0.003 0.049 4456 Dihedral : 13.697 88.660 10627 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3048 helix: 2.14 (0.22), residues: 669 sheet: 0.47 (0.18), residues: 730 loop : -1.10 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 644 TYR 0.015 0.001 TYR B 871 PHE 0.016 0.001 PHE B 904 TRP 0.015 0.001 TRP B 884 HIS 0.003 0.000 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00382 (25922) covalent geometry : angle 0.61269 (35273) SS BOND : bond 0.00316 ( 40) SS BOND : angle 1.60740 ( 80) hydrogen bonds : bond 0.12585 ( 1005) hydrogen bonds : angle 5.60298 ( 2733) link_BETA1-4 : bond 0.00386 ( 36) link_BETA1-4 : angle 1.88762 ( 108) link_NAG-ASN : bond 0.00304 ( 48) link_NAG-ASN : angle 2.07534 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8489 (m-80) cc_final: 0.8037 (m-80) REVERT: A 503 TYR cc_start: 0.7998 (t80) cc_final: 0.7745 (t80) REVERT: B 385 LEU cc_start: 0.9617 (mt) cc_final: 0.9403 (mm) REVERT: B 454 PHE cc_start: 0.8845 (m-80) cc_final: 0.8349 (m-80) REVERT: C 195 ILE cc_start: 0.9036 (mp) cc_final: 0.8733 (mp) outliers start: 0 outliers final: 1 residues processed: 94 average time/residue: 0.6364 time to fit residues: 70.5658 Evaluate side-chains 72 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 403 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.043616 restraints weight = 86611.328| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.11 r_work: 0.2563 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 26046 Z= 0.307 Angle : 0.695 9.160 35605 Z= 0.351 Chirality : 0.048 0.324 4250 Planarity : 0.004 0.052 4456 Dihedral : 8.152 72.236 5086 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 0.63 % Allowed : 6.64 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3048 helix: 1.89 (0.21), residues: 677 sheet: 0.38 (0.19), residues: 705 loop : -1.21 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1037 TYR 0.017 0.001 TYR B1065 PHE 0.033 0.002 PHE C 904 TRP 0.018 0.001 TRP B 884 HIS 0.004 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00735 (25922) covalent geometry : angle 0.67134 (35273) SS BOND : bond 0.00496 ( 40) SS BOND : angle 2.09421 ( 80) hydrogen bonds : bond 0.07432 ( 1005) hydrogen bonds : angle 5.31189 ( 2733) link_BETA1-4 : bond 0.00282 ( 36) link_BETA1-4 : angle 1.74665 ( 108) link_NAG-ASN : bond 0.00439 ( 48) link_NAG-ASN : angle 2.05481 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 TYR cc_start: 0.9136 (p90) cc_final: 0.8806 (p90) REVERT: A 372 PHE cc_start: 0.8774 (m-80) cc_final: 0.8222 (m-80) REVERT: A 503 TYR cc_start: 0.8139 (t80) cc_final: 0.7827 (t80) REVERT: A 1000 GLN cc_start: 0.9271 (tt0) cc_final: 0.9065 (tp40) REVERT: B 385 LEU cc_start: 0.9553 (mt) cc_final: 0.9140 (mm) REVERT: B 454 PHE cc_start: 0.9193 (m-80) cc_final: 0.8560 (m-80) outliers start: 17 outliers final: 4 residues processed: 75 average time/residue: 0.5780 time to fit residues: 51.9907 Evaluate side-chains 65 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain C residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 53 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 448 ASN B 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.073963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045196 restraints weight = 85295.937| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.03 r_work: 0.2608 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26046 Z= 0.154 Angle : 0.580 9.311 35605 Z= 0.293 Chirality : 0.045 0.301 4250 Planarity : 0.004 0.060 4456 Dihedral : 7.404 59.071 5084 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 1.03 % Allowed : 9.60 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3048 helix: 2.07 (0.21), residues: 676 sheet: 0.54 (0.19), residues: 714 loop : -1.15 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 406 TYR 0.017 0.001 TYR A 363 PHE 0.019 0.001 PHE A 390 TRP 0.013 0.001 TRP B 884 HIS 0.002 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00357 (25922) covalent geometry : angle 0.55761 (35273) SS BOND : bond 0.00367 ( 40) SS BOND : angle 1.63511 ( 80) hydrogen bonds : bond 0.06180 ( 1005) hydrogen bonds : angle 5.00687 ( 2733) link_BETA1-4 : bond 0.00341 ( 36) link_BETA1-4 : angle 1.67790 ( 108) link_NAG-ASN : bond 0.00280 ( 48) link_NAG-ASN : angle 1.86870 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 TYR cc_start: 0.9107 (p90) cc_final: 0.8768 (p90) REVERT: A 363 TYR cc_start: 0.9130 (m-80) cc_final: 0.8760 (m-80) REVERT: A 372 PHE cc_start: 0.8674 (m-80) cc_final: 0.8068 (m-80) REVERT: A 503 TYR cc_start: 0.8152 (t80) cc_final: 0.7813 (t80) REVERT: B 446 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8011 (p0) REVERT: B 454 PHE cc_start: 0.9166 (m-80) cc_final: 0.8561 (m-80) outliers start: 28 outliers final: 8 residues processed: 88 average time/residue: 0.5452 time to fit residues: 57.7212 Evaluate side-chains 72 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 272 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 243 optimal weight: 0.0270 chunk 282 optimal weight: 0.6980 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 499 ASN B 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.074034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.045092 restraints weight = 85135.661| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.09 r_work: 0.2609 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26046 Z= 0.155 Angle : 0.577 9.393 35605 Z= 0.289 Chirality : 0.045 0.296 4250 Planarity : 0.004 0.061 4456 Dihedral : 6.961 57.922 5084 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.59 % Favored : 95.24 % Rotamer: Outliers : 1.22 % Allowed : 11.55 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3048 helix: 2.10 (0.21), residues: 677 sheet: 0.63 (0.19), residues: 706 loop : -1.13 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.014 0.001 TYR B1065 PHE 0.013 0.001 PHE A 390 TRP 0.012 0.001 TRP B 884 HIS 0.002 0.001 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00364 (25922) covalent geometry : angle 0.55406 (35273) SS BOND : bond 0.00373 ( 40) SS BOND : angle 1.57306 ( 80) hydrogen bonds : bond 0.06044 ( 1005) hydrogen bonds : angle 4.91480 ( 2733) link_BETA1-4 : bond 0.00321 ( 36) link_BETA1-4 : angle 1.67657 ( 108) link_NAG-ASN : bond 0.00279 ( 48) link_NAG-ASN : angle 1.87817 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.9094 (m-80) cc_final: 0.8742 (m-80) REVERT: A 372 PHE cc_start: 0.8688 (m-80) cc_final: 0.8055 (m-80) REVERT: A 503 TYR cc_start: 0.8116 (t80) cc_final: 0.7759 (t80) REVERT: A 579 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8883 (p) REVERT: B 446 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7842 (p0) REVERT: B 454 PHE cc_start: 0.9168 (m-80) cc_final: 0.8568 (m-80) outliers start: 33 outliers final: 11 residues processed: 93 average time/residue: 0.4385 time to fit residues: 50.6113 Evaluate side-chains 76 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 776 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 116 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 760 GLN C 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.074410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.045675 restraints weight = 85218.327| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 4.03 r_work: 0.2630 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26046 Z= 0.129 Angle : 0.561 9.822 35605 Z= 0.280 Chirality : 0.044 0.300 4250 Planarity : 0.004 0.062 4456 Dihedral : 6.571 57.519 5084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.37 % Allowed : 12.26 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3048 helix: 2.15 (0.21), residues: 676 sheet: 0.68 (0.19), residues: 706 loop : -1.06 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 406 TYR 0.013 0.001 TYR C1065 PHE 0.011 0.001 PHE A1119 TRP 0.009 0.001 TRP B 884 HIS 0.002 0.000 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00295 (25922) covalent geometry : angle 0.53900 (35273) SS BOND : bond 0.00307 ( 40) SS BOND : angle 1.47116 ( 80) hydrogen bonds : bond 0.05679 ( 1005) hydrogen bonds : angle 4.81815 ( 2733) link_BETA1-4 : bond 0.00366 ( 36) link_BETA1-4 : angle 1.65717 ( 108) link_NAG-ASN : bond 0.00279 ( 48) link_NAG-ASN : angle 1.84204 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8648 (m-80) cc_final: 0.8004 (m-80) REVERT: A 579 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 983 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7540 (t0) REVERT: B 454 PHE cc_start: 0.9173 (m-80) cc_final: 0.8579 (m-80) REVERT: B 774 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9023 (ttmm) outliers start: 37 outliers final: 14 residues processed: 100 average time/residue: 0.4277 time to fit residues: 52.8047 Evaluate side-chains 81 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 1041 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 245 optimal weight: 0.2980 chunk 218 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.074015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.045050 restraints weight = 85733.490| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.08 r_work: 0.2607 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26046 Z= 0.164 Angle : 0.576 9.408 35605 Z= 0.288 Chirality : 0.045 0.304 4250 Planarity : 0.004 0.061 4456 Dihedral : 6.373 57.423 5084 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 1.85 % Allowed : 12.48 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3048 helix: 2.17 (0.21), residues: 673 sheet: 0.69 (0.19), residues: 694 loop : -1.09 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.014 0.001 TYR B1065 PHE 0.024 0.001 PHE A 390 TRP 0.010 0.001 TRP B 884 HIS 0.002 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00387 (25922) covalent geometry : angle 0.55396 (35273) SS BOND : bond 0.00341 ( 40) SS BOND : angle 1.56058 ( 80) hydrogen bonds : bond 0.05953 ( 1005) hydrogen bonds : angle 4.83648 ( 2733) link_BETA1-4 : bond 0.00321 ( 36) link_BETA1-4 : angle 1.67001 ( 108) link_NAG-ASN : bond 0.00283 ( 48) link_NAG-ASN : angle 1.87559 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 64 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8706 (m-80) cc_final: 0.8060 (m-80) REVERT: A 449 TYR cc_start: 0.7925 (m-80) cc_final: 0.6876 (t80) REVERT: A 579 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8876 (p) REVERT: A 757 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 983 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7541 (t0) REVERT: B 454 PHE cc_start: 0.9181 (m-80) cc_final: 0.8593 (m-80) REVERT: B 774 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9022 (ttmm) outliers start: 50 outliers final: 22 residues processed: 106 average time/residue: 0.4385 time to fit residues: 57.0094 Evaluate side-chains 89 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 1041 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 198 optimal weight: 0.0050 chunk 263 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.046614 restraints weight = 85104.259| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 4.06 r_work: 0.2654 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26046 Z= 0.106 Angle : 0.541 9.475 35605 Z= 0.269 Chirality : 0.044 0.309 4250 Planarity : 0.004 0.062 4456 Dihedral : 5.978 57.470 5084 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 1.22 % Allowed : 13.70 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3048 helix: 2.26 (0.21), residues: 671 sheet: 0.77 (0.19), residues: 699 loop : -1.00 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 406 TYR 0.014 0.001 TYR C1065 PHE 0.020 0.001 PHE A 390 TRP 0.009 0.001 TRP C 434 HIS 0.002 0.000 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00230 (25922) covalent geometry : angle 0.52037 (35273) SS BOND : bond 0.00272 ( 40) SS BOND : angle 1.27263 ( 80) hydrogen bonds : bond 0.05042 ( 1005) hydrogen bonds : angle 4.65970 ( 2733) link_BETA1-4 : bond 0.00419 ( 36) link_BETA1-4 : angle 1.62338 ( 108) link_NAG-ASN : bond 0.00307 ( 48) link_NAG-ASN : angle 1.78328 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8690 (m-80) cc_final: 0.8038 (m-80) REVERT: A 449 TYR cc_start: 0.7751 (m-80) cc_final: 0.6916 (t80) REVERT: A 561 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8907 (mp10) REVERT: A 579 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 757 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7956 (t80) REVERT: A 983 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7563 (t0) REVERT: B 454 PHE cc_start: 0.9173 (m-80) cc_final: 0.8589 (m-80) REVERT: B 774 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8787 (ttmm) outliers start: 33 outliers final: 16 residues processed: 100 average time/residue: 0.4489 time to fit residues: 55.0281 Evaluate side-chains 89 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 277 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 760 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.072564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.043405 restraints weight = 85673.963| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 4.07 r_work: 0.2551 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 26046 Z= 0.305 Angle : 0.677 9.533 35605 Z= 0.340 Chirality : 0.048 0.312 4250 Planarity : 0.004 0.066 4456 Dihedral : 6.356 58.226 5084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 1.92 % Allowed : 13.44 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3048 helix: 2.07 (0.21), residues: 672 sheet: 0.49 (0.19), residues: 666 loop : -1.14 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1037 TYR 0.015 0.001 TYR B1065 PHE 0.017 0.002 PHE A 390 TRP 0.014 0.001 TRP B 884 HIS 0.004 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00731 (25922) covalent geometry : angle 0.65281 (35273) SS BOND : bond 0.00477 ( 40) SS BOND : angle 2.05177 ( 80) hydrogen bonds : bond 0.07334 ( 1005) hydrogen bonds : angle 5.07124 ( 2733) link_BETA1-4 : bond 0.00269 ( 36) link_BETA1-4 : angle 1.77731 ( 108) link_NAG-ASN : bond 0.00449 ( 48) link_NAG-ASN : angle 2.04760 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 65 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8724 (m-80) cc_final: 0.8064 (m-80) REVERT: A 449 TYR cc_start: 0.7930 (m-80) cc_final: 0.7119 (t80) REVERT: A 579 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8836 (p) REVERT: A 757 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8173 (t80) REVERT: A 983 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7669 (t0) REVERT: B 321 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7273 (t) REVERT: B 454 PHE cc_start: 0.9169 (m-80) cc_final: 0.8593 (m-80) REVERT: B 491 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (pp30) outliers start: 52 outliers final: 26 residues processed: 111 average time/residue: 0.4500 time to fit residues: 61.9694 Evaluate side-chains 92 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1104 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 240 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.073838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.044866 restraints weight = 85293.722| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.07 r_work: 0.2600 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26046 Z= 0.143 Angle : 0.580 9.433 35605 Z= 0.291 Chirality : 0.045 0.310 4250 Planarity : 0.004 0.065 4456 Dihedral : 6.136 59.037 5084 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 1.33 % Allowed : 14.17 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3048 helix: 2.14 (0.21), residues: 673 sheet: 0.67 (0.19), residues: 689 loop : -1.08 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.014 0.001 TYR B1065 PHE 0.018 0.001 PHE A 390 TRP 0.010 0.001 TRP B 884 HIS 0.003 0.001 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00329 (25922) covalent geometry : angle 0.55758 (35273) SS BOND : bond 0.00336 ( 40) SS BOND : angle 1.60450 ( 80) hydrogen bonds : bond 0.06124 ( 1005) hydrogen bonds : angle 4.86449 ( 2733) link_BETA1-4 : bond 0.00368 ( 36) link_BETA1-4 : angle 1.66209 ( 108) link_NAG-ASN : bond 0.00288 ( 48) link_NAG-ASN : angle 1.85817 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8684 (m-80) cc_final: 0.8030 (m-80) REVERT: A 449 TYR cc_start: 0.7847 (m-80) cc_final: 0.6775 (t80) REVERT: A 561 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8760 (mp10) REVERT: A 579 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 757 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 983 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7671 (t0) REVERT: B 321 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7309 (t) REVERT: B 454 PHE cc_start: 0.9156 (m-80) cc_final: 0.8568 (m-80) REVERT: C 322 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8522 (pm20) outliers start: 36 outliers final: 20 residues processed: 99 average time/residue: 0.4419 time to fit residues: 53.6707 Evaluate side-chains 92 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1041 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 260 optimal weight: 0.1980 chunk 145 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 305 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.073939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.045079 restraints weight = 85046.494| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.06 r_work: 0.2609 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26046 Z= 0.147 Angle : 0.576 9.463 35605 Z= 0.288 Chirality : 0.045 0.309 4250 Planarity : 0.004 0.064 4456 Dihedral : 6.025 57.935 5084 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 1.26 % Allowed : 14.29 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3048 helix: 2.16 (0.21), residues: 676 sheet: 0.69 (0.19), residues: 689 loop : -1.06 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.014 0.001 TYR B1065 PHE 0.020 0.001 PHE A 390 TRP 0.009 0.001 TRP B 884 HIS 0.002 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00341 (25922) covalent geometry : angle 0.55418 (35273) SS BOND : bond 0.00327 ( 40) SS BOND : angle 1.56091 ( 80) hydrogen bonds : bond 0.05928 ( 1005) hydrogen bonds : angle 4.80588 ( 2733) link_BETA1-4 : bond 0.00341 ( 36) link_BETA1-4 : angle 1.66973 ( 108) link_NAG-ASN : bond 0.00280 ( 48) link_NAG-ASN : angle 1.85892 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8695 (m-80) cc_final: 0.8044 (m-80) REVERT: A 449 TYR cc_start: 0.7828 (m-80) cc_final: 0.6795 (t80) REVERT: A 561 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8734 (mp10) REVERT: A 579 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8860 (p) REVERT: A 757 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 983 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7661 (t0) REVERT: B 321 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7218 (t) REVERT: B 363 TYR cc_start: 0.9486 (m-80) cc_final: 0.9153 (m-80) REVERT: B 454 PHE cc_start: 0.9157 (m-80) cc_final: 0.8577 (m-80) REVERT: C 322 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8520 (pm20) outliers start: 34 outliers final: 21 residues processed: 95 average time/residue: 0.4529 time to fit residues: 53.2568 Evaluate side-chains 91 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1041 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 227 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 214 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 270 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.074374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045674 restraints weight = 84687.639| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.04 r_work: 0.2627 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26046 Z= 0.128 Angle : 0.560 9.509 35605 Z= 0.280 Chirality : 0.044 0.307 4250 Planarity : 0.004 0.062 4456 Dihedral : 5.874 57.421 5084 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer: Outliers : 1.14 % Allowed : 14.47 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3048 helix: 2.25 (0.21), residues: 670 sheet: 0.73 (0.19), residues: 689 loop : -1.02 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.013 0.001 TYR B1065 PHE 0.018 0.001 PHE A 390 TRP 0.009 0.001 TRP B 884 HIS 0.002 0.000 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00292 (25922) covalent geometry : angle 0.53833 (35273) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.44183 ( 80) hydrogen bonds : bond 0.05524 ( 1005) hydrogen bonds : angle 4.71836 ( 2733) link_BETA1-4 : bond 0.00373 ( 36) link_BETA1-4 : angle 1.64700 ( 108) link_NAG-ASN : bond 0.00282 ( 48) link_NAG-ASN : angle 1.81003 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7191.96 seconds wall clock time: 123 minutes 23.00 seconds (7403.00 seconds total)