Starting phenix.real_space_refine on Fri Feb 6 13:35:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7n_31775/02_2026/7v7n_31775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7n_31775/02_2026/7v7n_31775.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/7v7n_31775/02_2026/7v7n_31775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7n_31775/02_2026/7v7n_31775.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7n_31775/02_2026/7v7n_31775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7n_31775/02_2026/7v7n_31775.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= 0.038 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 16152 2.51 5 N 4139 2.21 5 O 5031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25430 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 6.31, per 1000 atoms: 0.25 Number of scatterers: 25430 At special positions: 0 Unit cell: (145.2, 148.5, 178.2, 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 5031 8.00 N 4139 7.00 C 16152 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=2.03 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=2.04 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=2.02 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=2.02 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=2.03 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=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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 329 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 329 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " 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 341 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 232 " " 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 25.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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 347 through 351 removed outlier: 3.577A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 388 removed outlier: 4.522A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.921A pdb=" N VAL A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.672A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.976A pdb=" N THR A 636 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 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 756 through 781 removed outlier: 3.645A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.502A pdb=" N LYS A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.779A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' 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 980 Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.186A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 4.009A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.119A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.685A 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 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.039A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.793A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.712A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.638A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.975A 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: 3.567A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' 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: 3.647A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.364A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 removed outlier: 3.577A pdb=" N GLU C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.721A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.607A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.765A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.591A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.500A pdb=" N SER C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.962A 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: 3.712A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.578A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.633A pdb=" N GLY C 887 " --> pdb=" O TRP C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.931A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 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 1032 removed outlier: 4.531A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.731A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.635A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.014A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.116A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.478A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 326 removed outlier: 5.097A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.590A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 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: 6.041A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.829A 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 removed outlier: 7.083A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.561A 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 26 through 30 removed outlier: 7.604A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.337A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.971A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.555A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.455A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.374A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.058A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.127A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.949A 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: 4.493A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 786 through 788 removed outlier: 5.745A pdb=" N ILE B 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.049A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 30 removed outlier: 8.391A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.919A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.069A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.582A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.892A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.212A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.810A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.598A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE9, first strand: chain 'C' and resid 1092 through 1095 993 hydrogen bonds defined for protein. 2709 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: 6.01 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8014 1.34 - 1.46: 6436 1.46 - 1.58: 11402 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25984 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.89e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 25979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 34301 1.60 - 3.20: 937 3.20 - 4.80: 89 4.80 - 6.41: 24 6.41 - 8.01: 6 Bond angle restraints: 35357 Sorted by residual: angle pdb=" C CYS A 660 " pdb=" N ASP A 661 " pdb=" CA ASP A 661 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.45 -3.75 1.22e+00 6.72e-01 9.45e+00 angle pdb=" N VAL C 339 " pdb=" CA VAL C 339 " pdb=" C VAL C 339 " ideal model delta sigma weight residual 113.39 109.20 4.19 1.47e+00 4.63e-01 8.14e+00 angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 122.29 117.99 4.30 1.65e+00 3.67e-01 6.80e+00 angle pdb=" C VAL B 481 " pdb=" N GLU B 482 " pdb=" CA GLU B 482 " ideal model delta sigma weight residual 121.76 127.45 -5.69 2.19e+00 2.09e-01 6.76e+00 ... (remaining 35352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 15394 21.60 - 43.19: 988 43.19 - 64.79: 166 64.79 - 86.38: 41 86.38 - 107.98: 9 Dihedral angle restraints: 16598 sinusoidal: 7571 harmonic: 9027 Sorted by residual: dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -2.39 -83.61 1 1.00e+01 1.00e-02 8.53e+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 -10.56 -75.44 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 536 " pdb=" SG CYS C 536 " pdb=" SG CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sinusoidal sigma weight residual -86.00 -11.49 -74.51 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 16595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4230 0.137 - 0.275: 26 0.275 - 0.412: 2 0.412 - 0.550: 1 0.550 - 0.687: 2 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.66e+00 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 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 4258 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.027 2.00e-02 2.50e+03 2.51e-02 7.90e+00 pdb=" CG ASN B1072 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " -0.001 2.00e-02 2.50e+03 2.26e-02 6.36e+00 pdb=" CG ASN B 232 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 904 " -0.019 2.00e-02 2.50e+03 1.75e-02 5.36e+00 pdb=" CG PHE C 904 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 904 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 904 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 904 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 904 " -0.001 2.00e-02 2.50e+03 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1156 2.72 - 3.26: 25010 3.26 - 3.81: 39404 3.81 - 4.35: 45870 4.35 - 4.90: 81156 Nonbonded interactions: 192596 Sorted by model distance: nonbonded pdb=" OD1 ASP C 566 " pdb=" OG1 THR C 570 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.190 3.040 nonbonded pdb=" O GLU A 154 " pdb=" OH TYR A 158 " model vdw 2.195 3.040 nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.211 3.040 nonbonded pdb=" O ARG A 212 " pdb=" OH TYR A 264 " model vdw 2.212 3.040 ... (remaining 192591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 619 or resid 631 through 2004)) selection = (chain 'B' and (resid 14 through 825 or resid 852 through 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 631 through 2004)) } ncs_group { reference = 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.330 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.005 0.053 26109 Z= 0.225 Angle : 0.661 13.572 35692 Z= 0.317 Chirality : 0.050 0.687 4261 Planarity : 0.004 0.043 4463 Dihedral : 13.977 107.980 10666 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.11 (0.15), residues: 3053 helix: 2.05 (0.22), residues: 646 sheet: 0.76 (0.19), residues: 721 loop : -1.08 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1037 TYR 0.019 0.001 TYR A 871 PHE 0.040 0.001 PHE C 904 TRP 0.024 0.001 TRP B 884 HIS 0.003 0.001 HIS C1056 Details of bonding type rmsd covalent geometry : bond 0.00495 (25984) covalent geometry : angle 0.61953 (35357) SS BOND : bond 0.00396 ( 40) SS BOND : angle 1.61997 ( 80) hydrogen bonds : bond 0.12281 ( 981) hydrogen bonds : angle 6.00593 ( 2709) link_BETA1-4 : bond 0.00465 ( 37) link_BETA1-4 : angle 2.06123 ( 111) link_NAG-ASN : bond 0.00392 ( 48) link_NAG-ASN : angle 3.05298 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8171 (t0) cc_final: 0.7906 (t0) REVERT: B 415 LYS cc_start: 0.9143 (tptm) cc_final: 0.8836 (tppt) REVERT: C 416 ILE cc_start: 0.9070 (mp) cc_final: 0.8841 (pp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.5645 time to fit residues: 74.1242 Evaluate side-chains 72 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0270 overall best weight: 1.6842 ------------------------------------------------------------------------------- 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** C 14 GLN C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049635 restraints weight = 86552.173| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.96 r_work: 0.2774 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26109 Z= 0.167 Angle : 0.608 13.226 35692 Z= 0.303 Chirality : 0.046 0.455 4261 Planarity : 0.004 0.060 4463 Dihedral : 8.321 72.438 5109 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 0.59 % Allowed : 6.74 % Favored : 92.67 % 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: 0.18 (0.15), residues: 3053 helix: 2.07 (0.22), residues: 659 sheet: 0.82 (0.19), residues: 697 loop : -1.03 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.023 0.001 PHE C 904 TRP 0.014 0.001 TRP A 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00387 (25984) covalent geometry : angle 0.57356 (35357) SS BOND : bond 0.00391 ( 40) SS BOND : angle 1.57823 ( 80) hydrogen bonds : bond 0.06178 ( 981) hydrogen bonds : angle 5.07330 ( 2709) link_BETA1-4 : bond 0.00393 ( 37) link_BETA1-4 : angle 1.81520 ( 111) link_NAG-ASN : bond 0.00349 ( 48) link_NAG-ASN : angle 2.62421 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8826 (t0) cc_final: 0.8466 (t0) REVERT: B 415 LYS cc_start: 0.9112 (tptm) cc_final: 0.8868 (tppt) REVERT: B 1027 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.9388 (tpp) REVERT: C 367 TYR cc_start: 0.8793 (t80) cc_final: 0.8529 (t80) REVERT: C 387 ASP cc_start: 0.9348 (t0) cc_final: 0.9126 (m-30) REVERT: C 454 PHE cc_start: 0.9146 (m-10) cc_final: 0.8849 (m-80) outliers start: 16 outliers final: 3 residues processed: 87 average time/residue: 0.6002 time to fit residues: 61.7063 Evaluate side-chains 75 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 778 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 233 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 ASN C1104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.079040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048858 restraints weight = 87123.647| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.01 r_work: 0.2743 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26109 Z= 0.197 Angle : 0.611 12.619 35692 Z= 0.305 Chirality : 0.046 0.475 4261 Planarity : 0.004 0.063 4463 Dihedral : 7.590 58.856 5109 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 1.07 % Allowed : 10.24 % Favored : 88.69 % 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: 0.12 (0.15), residues: 3053 helix: 1.99 (0.21), residues: 671 sheet: 0.71 (0.19), residues: 714 loop : -1.06 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 406 TYR 0.015 0.001 TYR A1065 PHE 0.023 0.001 PHE A 904 TRP 0.015 0.001 TRP A 884 HIS 0.004 0.001 HIS C1056 Details of bonding type rmsd covalent geometry : bond 0.00465 (25984) covalent geometry : angle 0.57754 (35357) SS BOND : bond 0.00405 ( 40) SS BOND : angle 1.58184 ( 80) hydrogen bonds : bond 0.06381 ( 981) hydrogen bonds : angle 5.00838 ( 2709) link_BETA1-4 : bond 0.00379 ( 37) link_BETA1-4 : angle 1.78825 ( 111) link_NAG-ASN : bond 0.00343 ( 48) link_NAG-ASN : angle 2.61232 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8881 (t0) cc_final: 0.8515 (t0) REVERT: B 415 LYS cc_start: 0.9193 (tptm) cc_final: 0.8970 (tppt) REVERT: B 471 TYR cc_start: 0.9028 (t80) cc_final: 0.8769 (t80) REVERT: B 856 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9169 (pp) REVERT: C 387 ASP cc_start: 0.9424 (t0) cc_final: 0.9173 (m-30) REVERT: C 406 ARG cc_start: 0.9039 (tmm160) cc_final: 0.8658 (ppt170) REVERT: C 421 TYR cc_start: 0.6371 (t80) cc_final: 0.6110 (t80) REVERT: C 453 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9014 (mt) REVERT: C 454 PHE cc_start: 0.9225 (m-10) cc_final: 0.8973 (m-80) REVERT: C 658 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8059 (p90) REVERT: C 988 GLU cc_start: 0.7896 (pm20) cc_final: 0.7611 (pm20) outliers start: 29 outliers final: 8 residues processed: 94 average time/residue: 0.5990 time to fit residues: 66.4331 Evaluate side-chains 80 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 778 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 56 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 256 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 306 optimal weight: 0.4980 chunk 278 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 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 = 0.3686 r_free = 0.3686 target = 0.079335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049259 restraints weight = 86589.925| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.99 r_work: 0.2756 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26109 Z= 0.158 Angle : 0.584 12.566 35692 Z= 0.291 Chirality : 0.045 0.478 4261 Planarity : 0.004 0.063 4463 Dihedral : 6.989 58.926 5109 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 1.44 % Allowed : 11.53 % Favored : 87.03 % 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: 3053 helix: 2.07 (0.21), residues: 670 sheet: 0.70 (0.19), residues: 710 loop : -1.02 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.015 0.001 TYR A1065 PHE 0.017 0.001 PHE C 904 TRP 0.015 0.001 TRP A 884 HIS 0.003 0.001 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00368 (25984) covalent geometry : angle 0.55083 (35357) SS BOND : bond 0.00349 ( 40) SS BOND : angle 1.45721 ( 80) hydrogen bonds : bond 0.05995 ( 981) hydrogen bonds : angle 4.88629 ( 2709) link_BETA1-4 : bond 0.00404 ( 37) link_BETA1-4 : angle 1.80395 ( 111) link_NAG-ASN : bond 0.00322 ( 48) link_NAG-ASN : angle 2.51803 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8938 (t0) cc_final: 0.8534 (t0) REVERT: B 415 LYS cc_start: 0.9207 (tptm) cc_final: 0.8974 (tppt) REVERT: B 471 TYR cc_start: 0.9059 (t80) cc_final: 0.8684 (t80) REVERT: B 856 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9136 (pp) REVERT: C 387 ASP cc_start: 0.9483 (t0) cc_final: 0.9206 (m-30) REVERT: C 453 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8935 (mt) REVERT: C 454 PHE cc_start: 0.9320 (m-10) cc_final: 0.8973 (m-80) REVERT: C 579 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8904 (p) REVERT: C 658 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7955 (p90) REVERT: C 974 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.8955 (t) REVERT: C 988 GLU cc_start: 0.7915 (pm20) cc_final: 0.7595 (pm20) outliers start: 39 outliers final: 13 residues processed: 108 average time/residue: 0.5645 time to fit residues: 73.2193 Evaluate side-chains 87 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 99 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 242 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 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 = 0.3684 r_free = 0.3684 target = 0.079153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049057 restraints weight = 86595.149| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.99 r_work: 0.2749 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26109 Z= 0.169 Angle : 0.592 12.452 35692 Z= 0.295 Chirality : 0.045 0.484 4261 Planarity : 0.004 0.064 4463 Dihedral : 6.749 58.600 5109 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.02 % Rotamer: Outliers : 1.44 % Allowed : 12.60 % Favored : 85.96 % 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: 0.18 (0.15), residues: 3053 helix: 2.07 (0.21), residues: 670 sheet: 0.71 (0.19), residues: 714 loop : -1.01 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 406 TYR 0.022 0.001 TYR C 378 PHE 0.020 0.001 PHE B 375 TRP 0.015 0.001 TRP A 884 HIS 0.003 0.001 HIS C1056 Details of bonding type rmsd covalent geometry : bond 0.00396 (25984) covalent geometry : angle 0.55914 (35357) SS BOND : bond 0.00367 ( 40) SS BOND : angle 1.55395 ( 80) hydrogen bonds : bond 0.06078 ( 981) hydrogen bonds : angle 4.88221 ( 2709) link_BETA1-4 : bond 0.00384 ( 37) link_BETA1-4 : angle 1.78252 ( 111) link_NAG-ASN : bond 0.00322 ( 48) link_NAG-ASN : angle 2.51504 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8924 (t0) cc_final: 0.8499 (t0) REVERT: B 415 LYS cc_start: 0.9184 (tptm) cc_final: 0.8955 (tppt) REVERT: B 471 TYR cc_start: 0.9116 (t80) cc_final: 0.8727 (t80) REVERT: B 579 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9183 (p) REVERT: B 856 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9132 (pp) REVERT: C 387 ASP cc_start: 0.9520 (t0) cc_final: 0.9211 (m-30) REVERT: C 406 ARG cc_start: 0.9192 (tmm-80) cc_final: 0.8952 (pmt-80) REVERT: C 421 TYR cc_start: 0.6268 (t80) cc_final: 0.6008 (t80) REVERT: C 453 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8939 (mt) REVERT: C 454 PHE cc_start: 0.9335 (m-10) cc_final: 0.8970 (m-80) REVERT: C 579 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8912 (p) REVERT: C 658 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.7866 (p90) REVERT: C 974 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9162 (p) REVERT: C 988 GLU cc_start: 0.7941 (pm20) cc_final: 0.7658 (pm20) outliers start: 39 outliers final: 15 residues processed: 105 average time/residue: 0.5371 time to fit residues: 67.5321 Evaluate side-chains 90 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 243 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 200 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 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 = 0.3696 r_free = 0.3696 target = 0.079722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049845 restraints weight = 86180.123| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.97 r_work: 0.2772 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26109 Z= 0.127 Angle : 0.567 12.428 35692 Z= 0.282 Chirality : 0.045 0.479 4261 Planarity : 0.004 0.063 4463 Dihedral : 6.471 57.751 5109 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 1.58 % Allowed : 13.52 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 3053 helix: 2.15 (0.21), residues: 674 sheet: 0.76 (0.19), residues: 707 loop : -0.95 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 406 TYR 0.016 0.001 TYR C 378 PHE 0.012 0.001 PHE A 398 TRP 0.012 0.001 TRP A 884 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00288 (25984) covalent geometry : angle 0.53496 (35357) SS BOND : bond 0.00350 ( 40) SS BOND : angle 1.37171 ( 80) hydrogen bonds : bond 0.05568 ( 981) hydrogen bonds : angle 4.76036 ( 2709) link_BETA1-4 : bond 0.00427 ( 37) link_BETA1-4 : angle 1.77269 ( 111) link_NAG-ASN : bond 0.00327 ( 48) link_NAG-ASN : angle 2.42304 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 79 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8895 (t0) cc_final: 0.8512 (t0) REVERT: B 453 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7434 (tm) REVERT: B 454 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: B 471 TYR cc_start: 0.9140 (t80) cc_final: 0.8843 (t80) REVERT: B 579 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9249 (p) REVERT: C 453 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8935 (mt) REVERT: C 454 PHE cc_start: 0.9317 (m-10) cc_final: 0.8955 (m-80) REVERT: C 579 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 658 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7717 (p90) REVERT: C 974 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9092 (p) REVERT: C 988 GLU cc_start: 0.7979 (pm20) cc_final: 0.7682 (pm20) outliers start: 43 outliers final: 12 residues processed: 114 average time/residue: 0.5383 time to fit residues: 73.5870 Evaluate side-chains 97 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 195 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 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 = 0.3692 r_free = 0.3692 target = 0.079518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049495 restraints weight = 86494.711| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.98 r_work: 0.2761 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26109 Z= 0.149 Angle : 0.590 12.258 35692 Z= 0.294 Chirality : 0.045 0.484 4261 Planarity : 0.004 0.062 4463 Dihedral : 6.353 56.088 5109 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 1.73 % Allowed : 14.11 % Favored : 84.16 % 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: 0.26 (0.16), residues: 3053 helix: 2.14 (0.21), residues: 674 sheet: 0.74 (0.19), residues: 707 loop : -0.95 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 406 TYR 0.015 0.001 TYR A1065 PHE 0.013 0.001 PHE A 398 TRP 0.012 0.001 TRP A 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00347 (25984) covalent geometry : angle 0.55894 (35357) SS BOND : bond 0.00402 ( 40) SS BOND : angle 1.42282 ( 80) hydrogen bonds : bond 0.05719 ( 981) hydrogen bonds : angle 4.76760 ( 2709) link_BETA1-4 : bond 0.00385 ( 37) link_BETA1-4 : angle 1.75958 ( 111) link_NAG-ASN : bond 0.00315 ( 48) link_NAG-ASN : angle 2.43321 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 82 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8933 (t0) cc_final: 0.8542 (t0) REVERT: B 415 LYS cc_start: 0.9187 (tppt) cc_final: 0.8898 (tptm) REVERT: B 471 TYR cc_start: 0.9149 (t80) cc_final: 0.8797 (t80) REVERT: B 579 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9204 (p) REVERT: C 387 ASP cc_start: 0.9422 (t0) cc_final: 0.9220 (m-30) REVERT: C 421 TYR cc_start: 0.6081 (t80) cc_final: 0.5776 (t80) REVERT: C 453 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8936 (mt) REVERT: C 454 PHE cc_start: 0.9313 (m-10) cc_final: 0.8948 (m-80) REVERT: C 579 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8904 (p) REVERT: C 658 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.7713 (p90) REVERT: C 974 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9026 (p) REVERT: C 988 GLU cc_start: 0.8016 (pm20) cc_final: 0.7713 (pm20) outliers start: 47 outliers final: 23 residues processed: 121 average time/residue: 0.5216 time to fit residues: 76.0839 Evaluate side-chains 102 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 0.0070 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 229 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 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 = 0.3700 r_free = 0.3700 target = 0.079934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050028 restraints weight = 86328.762| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.97 r_work: 0.2776 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26109 Z= 0.125 Angle : 0.585 12.264 35692 Z= 0.291 Chirality : 0.045 0.478 4261 Planarity : 0.004 0.102 4463 Dihedral : 6.222 56.210 5109 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 1.55 % Allowed : 14.55 % Favored : 83.90 % 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: 0.28 (0.16), residues: 3053 helix: 2.18 (0.21), residues: 679 sheet: 0.68 (0.19), residues: 721 loop : -0.92 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.012 0.001 PHE A 398 TRP 0.011 0.001 TRP A 884 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00283 (25984) covalent geometry : angle 0.55542 (35357) SS BOND : bond 0.00366 ( 40) SS BOND : angle 1.37422 ( 80) hydrogen bonds : bond 0.05440 ( 981) hydrogen bonds : angle 4.70447 ( 2709) link_BETA1-4 : bond 0.00422 ( 37) link_BETA1-4 : angle 1.74939 ( 111) link_NAG-ASN : bond 0.00326 ( 48) link_NAG-ASN : angle 2.38261 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8893 (t0) cc_final: 0.8530 (t0) REVERT: B 415 LYS cc_start: 0.9213 (tppt) cc_final: 0.8941 (tptm) REVERT: B 471 TYR cc_start: 0.9174 (t80) cc_final: 0.8864 (t80) REVERT: B 579 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9230 (p) REVERT: B 856 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8905 (pp) REVERT: C 387 ASP cc_start: 0.9415 (t0) cc_final: 0.9195 (m-30) REVERT: C 421 TYR cc_start: 0.6230 (t80) cc_final: 0.5947 (t80) REVERT: C 453 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8910 (mt) REVERT: C 454 PHE cc_start: 0.9291 (m-10) cc_final: 0.8932 (m-80) REVERT: C 579 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8894 (p) REVERT: C 658 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7670 (p90) REVERT: C 760 GLN cc_start: 0.8795 (mt0) cc_final: 0.8557 (mt0) REVERT: C 974 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9053 (p) REVERT: C 988 GLU cc_start: 0.8014 (pm20) cc_final: 0.7744 (pm20) outliers start: 42 outliers final: 24 residues processed: 122 average time/residue: 0.5526 time to fit residues: 80.7955 Evaluate side-chains 106 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 57 optimal weight: 0.0170 chunk 17 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 233 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.081159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051523 restraints weight = 86593.876| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.95 r_work: 0.2828 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26109 Z= 0.105 Angle : 0.575 12.093 35692 Z= 0.285 Chirality : 0.044 0.472 4261 Planarity : 0.004 0.067 4463 Dihedral : 5.948 56.273 5109 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 1.11 % Allowed : 15.22 % Favored : 83.68 % 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: 0.37 (0.16), residues: 3053 helix: 2.30 (0.22), residues: 676 sheet: 0.73 (0.19), residues: 715 loop : -0.89 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.017 0.001 PHE A 398 TRP 0.010 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00227 (25984) covalent geometry : angle 0.54799 (35357) SS BOND : bond 0.00285 ( 40) SS BOND : angle 1.05503 ( 80) hydrogen bonds : bond 0.04766 ( 981) hydrogen bonds : angle 4.54834 ( 2709) link_BETA1-4 : bond 0.00488 ( 37) link_BETA1-4 : angle 1.71673 ( 111) link_NAG-ASN : bond 0.00372 ( 48) link_NAG-ASN : angle 2.29445 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8907 (t0) cc_final: 0.8548 (t0) REVERT: B 52 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 415 LYS cc_start: 0.9264 (tppt) cc_final: 0.8966 (tptm) REVERT: B 454 PHE cc_start: 0.8304 (m-10) cc_final: 0.8038 (m-10) REVERT: B 471 TYR cc_start: 0.9115 (t80) cc_final: 0.8880 (t80) REVERT: B 579 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9267 (p) REVERT: B 856 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8830 (pp) REVERT: B 898 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9031 (mtp) REVERT: C 387 ASP cc_start: 0.9423 (t0) cc_final: 0.9183 (m-30) REVERT: C 406 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.8927 (pmt-80) REVERT: C 421 TYR cc_start: 0.6384 (t80) cc_final: 0.6164 (t80) REVERT: C 453 LEU cc_start: 0.9258 (tp) cc_final: 0.8987 (mt) REVERT: C 454 PHE cc_start: 0.9267 (m-10) cc_final: 0.8911 (m-80) REVERT: C 579 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8795 (p) REVERT: C 658 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7418 (p90) REVERT: C 974 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9027 (p) REVERT: C 988 GLU cc_start: 0.7915 (pm20) cc_final: 0.7688 (pm20) outliers start: 30 outliers final: 16 residues processed: 119 average time/residue: 0.5503 time to fit residues: 78.3956 Evaluate side-chains 104 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 262 optimal weight: 0.0020 chunk 301 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 238 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 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 = 0.3699 r_free = 0.3699 target = 0.079846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049778 restraints weight = 86652.746| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.00 r_work: 0.2768 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26109 Z= 0.159 Angle : 0.609 11.835 35692 Z= 0.302 Chirality : 0.045 0.474 4261 Planarity : 0.004 0.066 4463 Dihedral : 5.958 56.461 5109 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 1.03 % Allowed : 15.48 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 3053 helix: 2.26 (0.21), residues: 675 sheet: 0.79 (0.20), residues: 698 loop : -0.93 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.042 0.001 PHE B 375 TRP 0.013 0.001 TRP A 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00374 (25984) covalent geometry : angle 0.58083 (35357) SS BOND : bond 0.00404 ( 40) SS BOND : angle 1.44779 ( 80) hydrogen bonds : bond 0.05561 ( 981) hydrogen bonds : angle 4.65826 ( 2709) link_BETA1-4 : bond 0.00366 ( 37) link_BETA1-4 : angle 1.70283 ( 111) link_NAG-ASN : bond 0.00307 ( 48) link_NAG-ASN : angle 2.37880 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8914 (t0) cc_final: 0.8525 (t0) REVERT: B 52 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8491 (tm-30) REVERT: B 415 LYS cc_start: 0.9273 (tppt) cc_final: 0.8931 (tptm) REVERT: B 471 TYR cc_start: 0.9117 (t80) cc_final: 0.8910 (t80) REVERT: B 579 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9218 (p) REVERT: B 856 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8903 (pp) REVERT: B 898 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.9129 (mtp) REVERT: C 387 ASP cc_start: 0.9478 (t0) cc_final: 0.9226 (m-30) REVERT: C 406 ARG cc_start: 0.9216 (tmm-80) cc_final: 0.8947 (pmt-80) REVERT: C 421 TYR cc_start: 0.6519 (t80) cc_final: 0.6284 (t80) REVERT: C 453 LEU cc_start: 0.9254 (tp) cc_final: 0.8974 (mt) REVERT: C 454 PHE cc_start: 0.9274 (m-10) cc_final: 0.8914 (m-80) REVERT: C 579 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8763 (p) REVERT: C 658 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.7775 (p90) REVERT: C 974 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9023 (p) REVERT: C 988 GLU cc_start: 0.8040 (pm20) cc_final: 0.7772 (pm20) outliers start: 28 outliers final: 17 residues processed: 105 average time/residue: 0.5945 time to fit residues: 74.3000 Evaluate side-chains 97 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 199 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 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 = 0.3701 r_free = 0.3701 target = 0.079982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049890 restraints weight = 86226.051| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.98 r_work: 0.2772 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26109 Z= 0.143 Angle : 0.602 11.861 35692 Z= 0.299 Chirality : 0.045 0.469 4261 Planarity : 0.004 0.067 4463 Dihedral : 5.944 55.977 5109 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 1.11 % Allowed : 15.51 % Favored : 83.38 % 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: 0.29 (0.16), residues: 3053 helix: 2.21 (0.21), residues: 678 sheet: 0.64 (0.19), residues: 726 loop : -0.92 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.015 0.001 PHE A 398 TRP 0.013 0.001 TRP A 884 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00334 (25984) covalent geometry : angle 0.57471 (35357) SS BOND : bond 0.00354 ( 40) SS BOND : angle 1.36564 ( 80) hydrogen bonds : bond 0.05531 ( 981) hydrogen bonds : angle 4.66665 ( 2709) link_BETA1-4 : bond 0.00404 ( 37) link_BETA1-4 : angle 1.69971 ( 111) link_NAG-ASN : bond 0.00311 ( 48) link_NAG-ASN : angle 2.34672 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6895.00 seconds wall clock time: 118 minutes 47.50 seconds (7127.50 seconds total)