Starting phenix.real_space_refine on Thu Mar 5 21:33:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7t_31781/03_2026/7v7t_31781.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7t_31781/03_2026/7v7t_31781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7t_31781/03_2026/7v7t_31781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7t_31781/03_2026/7v7t_31781.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7t_31781/03_2026/7v7t_31781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7t_31781/03_2026/7v7t_31781.cif" } resolution = 3.0 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= 0.054 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 16060 2.51 5 N 4116 2.21 5 O 5006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25290 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} 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: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.59, per 1000 atoms: 0.22 Number of scatterers: 25290 At special positions: 0 Unit cell: (141.9, 145.2, 198, 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 5006 8.00 N 4116 7.00 C 16060 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.02 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 341 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 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 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 329 " " NAG f 1 " - " ASN C 614 " " NAG g 1 " - " ASN C 707 " " NAG h 1 " - " ASN C 715 " " NAG i 1 " - " ASN C 799 " " NAG j 1 " - " ASN C1072 " " NAG k 1 " - " ASN C1096 " " NAG l 1 " - " ASN C1132 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 47 sheets defined 24.6% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.320A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.833A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 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 757 through 781 removed outlier: 4.094A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.511A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.560A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.294A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.506A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.557A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.329A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 4.004A 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 347 through 351 removed outlier: 3.872A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.068A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 404 through 408 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 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.780A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.635A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.616A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.002A 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: 3.643A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.762A 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 982 removed outlier: 3.652A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.311A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.728A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.536A pdb=" N PHE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 336 through 341' Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.528A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.161A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.913A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.326A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.516A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.885A pdb=" N TYR C 902 " --> pdb=" O MET C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.296A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) 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 982 removed outlier: 3.578A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.891A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.827A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.742A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 574 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.868A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.221A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.562A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.721A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 7.248A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 574 removed outlier: 3.676A pdb=" N ALA A 573 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.012A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.914A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.550A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.587A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.710A pdb=" N ILE A 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.633A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.841A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.346A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.532A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.480A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC8, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.372A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AD1, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD2, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.079A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 699 through 701 removed outlier: 7.111A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.080A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.535A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD7, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.106A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.691A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.023A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.222A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.962A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE4, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE5, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE6, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.822A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.602A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.531A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF2, first strand: chain 'C' and resid 1092 through 1095 989 hydrogen bonds defined for protein. 2712 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: 5.79 Time building geometry restraints manager: 2.96 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: 7980 1.34 - 1.46: 6447 1.46 - 1.58: 11278 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25837 Sorted by residual: bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 ... (remaining 25832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 34293 1.73 - 3.46: 790 3.46 - 5.19: 53 5.19 - 6.92: 14 6.92 - 8.65: 7 Bond angle restraints: 35157 Sorted by residual: angle pdb=" N THR C 616 " pdb=" CA THR C 616 " pdb=" C THR C 616 " ideal model delta sigma weight residual 114.56 109.19 5.37 1.27e+00 6.20e-01 1.79e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.58 -3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.90 -6.43 2.06e+00 2.36e-01 9.76e+00 angle pdb=" C ASN A 232 " pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 120.49 124.53 -4.04 1.38e+00 5.25e-01 8.55e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.18 -5.71 2.06e+00 2.36e-01 7.69e+00 ... (remaining 35152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 15192 20.64 - 41.27: 1065 41.27 - 61.91: 176 61.91 - 82.54: 40 82.54 - 103.18: 15 Dihedral angle restraints: 16488 sinusoidal: 7498 harmonic: 8990 Sorted by residual: dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 1.73 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS C1080 " pdb=" SG CYS C1080 " pdb=" SG CYS C1124 " pdb=" CB CYS C1124 " ideal model delta sinusoidal sigma weight residual 93.00 7.49 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -169.91 83.91 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 16485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4217 0.151 - 0.303: 17 0.303 - 0.454: 1 0.454 - 0.606: 0 0.606 - 0.757: 1 Chirality restraints: 4236 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 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 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4233 not shown) Planarity restraints: 4493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO C 984 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 984 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1137 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A1138 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1138 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1138 " -0.027 5.00e-02 4.00e+02 ... (remaining 4490 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 724 2.70 - 3.25: 24287 3.25 - 3.80: 38354 3.80 - 4.35: 47416 4.35 - 4.90: 82148 Nonbonded interactions: 192929 Sorted by model distance: nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.174 3.040 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 189 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN A 802 " pdb=" O6 NAG L 1 " model vdw 2.219 3.040 ... (remaining 192924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 23.980 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25960 Z= 0.181 Angle : 0.626 17.562 35486 Z= 0.298 Chirality : 0.048 0.757 4236 Planarity : 0.004 0.061 4445 Dihedral : 13.854 103.181 10580 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3041 helix: 2.20 (0.21), residues: 667 sheet: 0.59 (0.19), residues: 715 loop : -1.08 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 188 TYR 0.017 0.001 TYR A 871 PHE 0.026 0.001 PHE A 904 TRP 0.019 0.001 TRP C 434 HIS 0.002 0.000 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00373 (25837) covalent geometry : angle 0.58932 (35157) SS BOND : bond 0.00311 ( 40) SS BOND : angle 1.66051 ( 80) hydrogen bonds : bond 0.11011 ( 989) hydrogen bonds : angle 5.47324 ( 2712) link_BETA1-4 : bond 0.00379 ( 35) link_BETA1-4 : angle 2.03273 ( 105) link_NAG-ASN : bond 0.00398 ( 48) link_NAG-ASN : angle 2.69828 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8927 (mp) cc_final: 0.8500 (tp) REVERT: B 52 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 81 ASN cc_start: 0.8399 (m-40) cc_final: 0.8111 (p0) REVERT: B 133 PHE cc_start: 0.8642 (m-80) cc_final: 0.8353 (m-80) REVERT: B 419 TYR cc_start: 0.9050 (m-10) cc_final: 0.8529 (m-10) REVERT: C 64 TRP cc_start: 0.7204 (t60) cc_final: 0.6652 (t60) REVERT: C 133 PHE cc_start: 0.8058 (m-80) cc_final: 0.7706 (m-80) REVERT: C 195 ILE cc_start: 0.8650 (tp) cc_final: 0.8405 (tp) REVERT: C 1000 GLN cc_start: 0.8061 (tp40) cc_final: 0.7702 (tp-100) outliers start: 0 outliers final: 2 residues processed: 171 average time/residue: 0.6092 time to fit residues: 122.0994 Evaluate side-chains 101 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain C residue 866 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN B 392 ASN C 115 GLN C 604 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092111 restraints weight = 48935.832| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.99 r_work: 0.2945 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25960 Z= 0.171 Angle : 0.621 9.433 35486 Z= 0.307 Chirality : 0.046 0.331 4236 Planarity : 0.004 0.064 4445 Dihedral : 8.268 171.761 5060 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 0.89 % Allowed : 7.59 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3041 helix: 2.15 (0.21), residues: 666 sheet: 0.71 (0.19), residues: 699 loop : -1.09 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 212 TYR 0.021 0.001 TYR C1065 PHE 0.025 0.001 PHE A 904 TRP 0.015 0.001 TRP C 434 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00411 (25837) covalent geometry : angle 0.59560 (35157) SS BOND : bond 0.00377 ( 40) SS BOND : angle 1.69087 ( 80) hydrogen bonds : bond 0.05735 ( 989) hydrogen bonds : angle 4.87885 ( 2712) link_BETA1-4 : bond 0.00446 ( 35) link_BETA1-4 : angle 1.86362 ( 105) link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 2.04988 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8927 (mp) cc_final: 0.8501 (tp) REVERT: A 738 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8602 (ttt) REVERT: B 115 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7945 (tp-100) REVERT: B 133 PHE cc_start: 0.8606 (m-80) cc_final: 0.8325 (m-80) REVERT: B 240 LEU cc_start: 0.8345 (mp) cc_final: 0.7727 (tp) REVERT: C 771 GLU cc_start: 0.8471 (tp30) cc_final: 0.7861 (tt0) REVERT: C 772 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7781 (mp-120) REVERT: C 1000 GLN cc_start: 0.8567 (tp40) cc_final: 0.8093 (tp-100) REVERT: C 1098 THR cc_start: 0.8701 (m) cc_final: 0.8424 (p) outliers start: 24 outliers final: 11 residues processed: 120 average time/residue: 0.5440 time to fit residues: 78.4749 Evaluate side-chains 107 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 130 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 292 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 899 GLN C 162 ASN C 332 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.144797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085685 restraints weight = 46721.740| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.86 r_work: 0.2989 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25960 Z= 0.126 Angle : 0.571 9.526 35486 Z= 0.282 Chirality : 0.045 0.338 4236 Planarity : 0.004 0.059 4445 Dihedral : 7.260 84.854 5054 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 1.41 % Allowed : 9.73 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3041 helix: 2.24 (0.21), residues: 666 sheet: 0.76 (0.19), residues: 702 loop : -1.05 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 212 TYR 0.018 0.001 TYR C1065 PHE 0.016 0.001 PHE B 390 TRP 0.013 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00291 (25837) covalent geometry : angle 0.54622 (35157) SS BOND : bond 0.00309 ( 40) SS BOND : angle 1.42886 ( 80) hydrogen bonds : bond 0.05196 ( 989) hydrogen bonds : angle 4.70264 ( 2712) link_BETA1-4 : bond 0.00392 ( 35) link_BETA1-4 : angle 1.81172 ( 105) link_NAG-ASN : bond 0.00307 ( 48) link_NAG-ASN : angle 2.02237 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.8663 (t) cc_final: 0.8437 (p) REVERT: A 240 LEU cc_start: 0.8952 (mp) cc_final: 0.8495 (tp) REVERT: A 1027 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8213 (ttp) REVERT: B 115 GLN cc_start: 0.8317 (tp-100) cc_final: 0.8084 (tp-100) REVERT: B 133 PHE cc_start: 0.8650 (m-80) cc_final: 0.8375 (m-80) REVERT: B 240 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7865 (tp) REVERT: B 422 LYS cc_start: 0.8286 (tptp) cc_final: 0.8083 (tppp) REVERT: C 771 GLU cc_start: 0.8398 (tp30) cc_final: 0.7837 (tt0) REVERT: C 772 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7648 (mp-120) REVERT: C 1000 GLN cc_start: 0.8600 (tp40) cc_final: 0.8023 (tp-100) REVERT: C 1098 THR cc_start: 0.8755 (m) cc_final: 0.8466 (p) outliers start: 38 outliers final: 16 residues processed: 132 average time/residue: 0.4536 time to fit residues: 73.5503 Evaluate side-chains 111 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 173 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 235 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1009 GLN C 162 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.148507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089531 restraints weight = 48948.785| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.84 r_work: 0.2890 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25960 Z= 0.264 Angle : 0.675 9.905 35486 Z= 0.336 Chirality : 0.049 0.335 4236 Planarity : 0.004 0.056 4445 Dihedral : 7.168 80.282 5054 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 1.85 % Allowed : 12.62 % Favored : 85.53 % 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: -0.04 (0.15), residues: 3041 helix: 2.01 (0.21), residues: 669 sheet: 0.60 (0.19), residues: 683 loop : -1.20 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1037 TYR 0.027 0.002 TYR B1065 PHE 0.032 0.002 PHE C1119 TRP 0.020 0.002 TRP B 884 HIS 0.007 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00650 (25837) covalent geometry : angle 0.64761 (35157) SS BOND : bond 0.00482 ( 40) SS BOND : angle 1.90817 ( 80) hydrogen bonds : bond 0.07044 ( 989) hydrogen bonds : angle 5.04263 ( 2712) link_BETA1-4 : bond 0.00319 ( 35) link_BETA1-4 : angle 1.93786 ( 105) link_NAG-ASN : bond 0.00314 ( 48) link_NAG-ASN : angle 2.24999 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8060 (t) REVERT: A 240 LEU cc_start: 0.9017 (mp) cc_final: 0.8528 (tp) REVERT: A 652 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: B 115 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7942 (tp40) REVERT: B 133 PHE cc_start: 0.8631 (m-80) cc_final: 0.8386 (m-80) REVERT: B 240 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7839 (tp) REVERT: B 307 GLU cc_start: 0.8123 (mp0) cc_final: 0.7820 (pm20) REVERT: B 422 LYS cc_start: 0.8193 (tptp) cc_final: 0.7992 (tppp) REVERT: C 558 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 1000 GLN cc_start: 0.8788 (tp40) cc_final: 0.8188 (tp-100) outliers start: 50 outliers final: 24 residues processed: 132 average time/residue: 0.5089 time to fit residues: 81.1467 Evaluate side-chains 114 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 226 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN C 162 ASN ** C 639 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 = 0.4076 r_free = 0.4076 target = 0.145396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.088358 restraints weight = 48496.247| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.33 r_work: 0.2954 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25960 Z= 0.175 Angle : 0.609 9.850 35486 Z= 0.301 Chirality : 0.046 0.343 4236 Planarity : 0.004 0.052 4445 Dihedral : 6.830 77.253 5054 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer: Outliers : 2.15 % Allowed : 13.73 % Favored : 84.12 % 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: -0.02 (0.15), residues: 3041 helix: 2.07 (0.21), residues: 676 sheet: 0.60 (0.19), residues: 688 loop : -1.22 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1037 TYR 0.020 0.001 TYR C1065 PHE 0.025 0.001 PHE C 133 TRP 0.015 0.001 TRP B 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00423 (25837) covalent geometry : angle 0.58175 (35157) SS BOND : bond 0.00373 ( 40) SS BOND : angle 1.67629 ( 80) hydrogen bonds : bond 0.06136 ( 989) hydrogen bonds : angle 4.87994 ( 2712) link_BETA1-4 : bond 0.00350 ( 35) link_BETA1-4 : angle 1.87011 ( 105) link_NAG-ASN : bond 0.00282 ( 48) link_NAG-ASN : angle 2.14103 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 94 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7969 (t) REVERT: A 240 LEU cc_start: 0.8995 (mp) cc_final: 0.8538 (tp) REVERT: A 584 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: A 652 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 738 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8574 (ttt) REVERT: B 115 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7947 (tp40) REVERT: B 133 PHE cc_start: 0.8641 (m-80) cc_final: 0.8414 (m-80) REVERT: B 240 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7847 (tp) REVERT: B 307 GLU cc_start: 0.8106 (mp0) cc_final: 0.7856 (pm20) REVERT: B 422 LYS cc_start: 0.8318 (tptp) cc_final: 0.8100 (tppp) REVERT: C 210 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8103 (tm) REVERT: C 558 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8776 (mp) REVERT: C 771 GLU cc_start: 0.8495 (tp30) cc_final: 0.7988 (tt0) REVERT: C 772 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7914 (mp-120) REVERT: C 1000 GLN cc_start: 0.8726 (tp40) cc_final: 0.8305 (tm-30) outliers start: 58 outliers final: 25 residues processed: 143 average time/residue: 0.4026 time to fit residues: 71.2556 Evaluate side-chains 121 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 170 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.146582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089924 restraints weight = 48568.962| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.33 r_work: 0.2983 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25960 Z= 0.129 Angle : 0.576 9.654 35486 Z= 0.284 Chirality : 0.045 0.346 4236 Planarity : 0.004 0.050 4445 Dihedral : 6.437 71.922 5054 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 1.92 % Allowed : 14.58 % 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: 0.11 (0.15), residues: 3041 helix: 2.28 (0.21), residues: 669 sheet: 0.67 (0.19), residues: 696 loop : -1.17 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 212 TYR 0.017 0.001 TYR C1065 PHE 0.022 0.001 PHE C 133 TRP 0.013 0.001 TRP C 434 HIS 0.004 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00298 (25837) covalent geometry : angle 0.55042 (35157) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.45733 ( 80) hydrogen bonds : bond 0.05395 ( 989) hydrogen bonds : angle 4.71697 ( 2712) link_BETA1-4 : bond 0.00387 ( 35) link_BETA1-4 : angle 1.84029 ( 105) link_NAG-ASN : bond 0.00301 ( 48) link_NAG-ASN : angle 2.05915 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8294 (m-10) cc_final: 0.7767 (m-80) REVERT: A 203 SER cc_start: 0.8663 (t) cc_final: 0.8463 (p) REVERT: A 240 LEU cc_start: 0.9007 (mp) cc_final: 0.8542 (tp) REVERT: A 584 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: A 652 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: B 115 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7931 (tp40) REVERT: B 240 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7884 (tp) REVERT: B 422 LYS cc_start: 0.8433 (tptp) cc_final: 0.8222 (tppp) REVERT: C 771 GLU cc_start: 0.8452 (tp30) cc_final: 0.7867 (tt0) REVERT: C 772 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7669 (mp-120) REVERT: C 1000 GLN cc_start: 0.8695 (tp40) cc_final: 0.8262 (tm-30) REVERT: C 1098 THR cc_start: 0.8857 (m) cc_final: 0.8553 (p) outliers start: 52 outliers final: 28 residues processed: 142 average time/residue: 0.4167 time to fit residues: 73.2678 Evaluate side-chains 123 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 297 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 chunk 187 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.146959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090235 restraints weight = 48370.475| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.33 r_work: 0.2988 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25960 Z= 0.126 Angle : 0.579 9.612 35486 Z= 0.283 Chirality : 0.045 0.345 4236 Planarity : 0.004 0.049 4445 Dihedral : 6.193 65.566 5054 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 1.63 % Allowed : 15.54 % Favored : 82.83 % 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: 0.17 (0.15), residues: 3041 helix: 2.34 (0.21), residues: 663 sheet: 0.69 (0.19), residues: 702 loop : -1.13 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 212 TYR 0.017 0.001 TYR C1065 PHE 0.020 0.001 PHE B 133 TRP 0.012 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00293 (25837) covalent geometry : angle 0.55356 (35157) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.45168 ( 80) hydrogen bonds : bond 0.05224 ( 989) hydrogen bonds : angle 4.65599 ( 2712) link_BETA1-4 : bond 0.00385 ( 35) link_BETA1-4 : angle 1.83286 ( 105) link_NAG-ASN : bond 0.00295 ( 48) link_NAG-ASN : angle 2.03440 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8301 (m-10) cc_final: 0.7781 (m-80) REVERT: A 240 LEU cc_start: 0.9011 (mp) cc_final: 0.8556 (tp) REVERT: A 738 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8583 (ttt) REVERT: A 1027 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8379 (ttp) REVERT: B 115 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7862 (tp40) REVERT: B 240 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7882 (tp) REVERT: C 229 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (mp) REVERT: C 771 GLU cc_start: 0.8456 (tp30) cc_final: 0.7887 (tt0) REVERT: C 772 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7650 (mp-120) REVERT: C 1000 GLN cc_start: 0.8674 (tp40) cc_final: 0.8245 (tm-30) REVERT: C 1098 THR cc_start: 0.8852 (m) cc_final: 0.8564 (p) outliers start: 44 outliers final: 27 residues processed: 129 average time/residue: 0.4473 time to fit residues: 70.7962 Evaluate side-chains 123 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 239 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 236 optimal weight: 5.9990 chunk 46 optimal weight: 0.0060 chunk 180 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.144075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085182 restraints weight = 46371.207| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.84 r_work: 0.3018 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25960 Z= 0.117 Angle : 0.572 10.068 35486 Z= 0.279 Chirality : 0.045 0.344 4236 Planarity : 0.004 0.047 4445 Dihedral : 5.953 59.031 5054 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 1.63 % Allowed : 15.69 % Favored : 82.68 % 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: 0.22 (0.15), residues: 3041 helix: 2.37 (0.21), residues: 663 sheet: 0.74 (0.19), residues: 705 loop : -1.11 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.017 0.001 TYR C1065 PHE 0.026 0.001 PHE C 133 TRP 0.012 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00268 (25837) covalent geometry : angle 0.54761 (35157) SS BOND : bond 0.00281 ( 40) SS BOND : angle 1.38565 ( 80) hydrogen bonds : bond 0.04974 ( 989) hydrogen bonds : angle 4.58830 ( 2712) link_BETA1-4 : bond 0.00403 ( 35) link_BETA1-4 : angle 1.81886 ( 105) link_NAG-ASN : bond 0.00301 ( 48) link_NAG-ASN : angle 1.99703 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8266 (m-10) cc_final: 0.7831 (m-80) REVERT: A 240 LEU cc_start: 0.8971 (mp) cc_final: 0.8567 (tp) REVERT: A 738 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8590 (ttt) REVERT: A 1027 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: B 52 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 115 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7804 (tp40) REVERT: B 133 PHE cc_start: 0.8596 (m-80) cc_final: 0.8003 (m-10) REVERT: B 135 PHE cc_start: 0.7514 (m-80) cc_final: 0.7282 (m-80) REVERT: B 240 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7871 (tp) REVERT: B 1037 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8956 (mtp180) REVERT: C 229 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8198 (mp) REVERT: C 659 GLU cc_start: 0.7983 (tp30) cc_final: 0.7744 (tp30) REVERT: C 771 GLU cc_start: 0.8425 (tp30) cc_final: 0.7857 (tt0) REVERT: C 772 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7587 (mp-120) REVERT: C 1000 GLN cc_start: 0.8643 (tp40) cc_final: 0.8191 (tm-30) REVERT: C 1098 THR cc_start: 0.8856 (m) cc_final: 0.8593 (p) outliers start: 44 outliers final: 27 residues processed: 129 average time/residue: 0.4356 time to fit residues: 69.1774 Evaluate side-chains 122 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 220 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 199 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.146129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089481 restraints weight = 48347.675| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.31 r_work: 0.2970 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25960 Z= 0.158 Angle : 0.598 9.640 35486 Z= 0.292 Chirality : 0.045 0.339 4236 Planarity : 0.004 0.048 4445 Dihedral : 5.914 56.933 5054 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 1.63 % Allowed : 15.84 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3041 helix: 2.38 (0.21), residues: 663 sheet: 0.66 (0.19), residues: 697 loop : -1.15 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1037 TYR 0.020 0.001 TYR C1065 PHE 0.023 0.001 PHE C 133 TRP 0.012 0.001 TRP B 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00382 (25837) covalent geometry : angle 0.57269 (35157) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.56678 ( 80) hydrogen bonds : bond 0.05514 ( 989) hydrogen bonds : angle 4.66723 ( 2712) link_BETA1-4 : bond 0.00361 ( 35) link_BETA1-4 : angle 1.85448 ( 105) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 2.03674 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8273 (m-10) cc_final: 0.7844 (m-80) REVERT: A 240 LEU cc_start: 0.8986 (mp) cc_final: 0.8606 (tp) REVERT: A 738 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8591 (ttt) REVERT: A 1027 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8387 (ttp) REVERT: B 115 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7840 (tp40) REVERT: B 133 PHE cc_start: 0.8548 (m-80) cc_final: 0.7951 (m-10) REVERT: B 135 PHE cc_start: 0.7506 (m-80) cc_final: 0.7285 (m-80) REVERT: B 240 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7832 (tp) REVERT: B 1037 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8909 (mtp180) REVERT: C 229 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8228 (mp) REVERT: C 771 GLU cc_start: 0.8490 (tp30) cc_final: 0.7913 (tt0) REVERT: C 772 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7652 (mp-120) REVERT: C 1000 GLN cc_start: 0.8706 (tp40) cc_final: 0.8269 (tm-30) REVERT: C 1098 THR cc_start: 0.8865 (m) cc_final: 0.8555 (p) outliers start: 44 outliers final: 29 residues processed: 125 average time/residue: 0.4485 time to fit residues: 69.3062 Evaluate side-chains 121 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 186 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 290 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.146791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089895 restraints weight = 48572.911| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.34 r_work: 0.2983 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25960 Z= 0.137 Angle : 0.595 9.633 35486 Z= 0.290 Chirality : 0.045 0.339 4236 Planarity : 0.004 0.048 4445 Dihedral : 5.810 56.334 5054 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 1.41 % Allowed : 16.14 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3041 helix: 2.41 (0.21), residues: 657 sheet: 0.69 (0.19), residues: 697 loop : -1.12 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 212 TYR 0.018 0.001 TYR C1065 PHE 0.017 0.001 PHE C1119 TRP 0.022 0.001 TRP C 64 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00324 (25837) covalent geometry : angle 0.56947 (35157) SS BOND : bond 0.00300 ( 40) SS BOND : angle 1.66756 ( 80) hydrogen bonds : bond 0.05298 ( 989) hydrogen bonds : angle 4.63622 ( 2712) link_BETA1-4 : bond 0.00379 ( 35) link_BETA1-4 : angle 1.84642 ( 105) link_NAG-ASN : bond 0.00293 ( 48) link_NAG-ASN : angle 2.01873 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8287 (m-10) cc_final: 0.7772 (m-80) REVERT: A 240 LEU cc_start: 0.8979 (mp) cc_final: 0.8608 (tp) REVERT: A 738 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8625 (ttt) REVERT: A 1027 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8353 (ttp) REVERT: B 115 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7843 (tp40) REVERT: B 133 PHE cc_start: 0.8526 (m-80) cc_final: 0.7888 (m-10) REVERT: B 135 PHE cc_start: 0.7518 (m-80) cc_final: 0.7293 (m-80) REVERT: B 240 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7846 (tp) REVERT: B 1037 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8951 (mtp180) REVERT: C 229 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 771 GLU cc_start: 0.8459 (tp30) cc_final: 0.7889 (tt0) REVERT: C 772 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7633 (mp-120) REVERT: C 1000 GLN cc_start: 0.8684 (tp40) cc_final: 0.8255 (tm-30) REVERT: C 1098 THR cc_start: 0.8878 (m) cc_final: 0.8592 (p) outliers start: 38 outliers final: 28 residues processed: 119 average time/residue: 0.4422 time to fit residues: 65.0249 Evaluate side-chains 119 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 103 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 219 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.147342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.090815 restraints weight = 48317.684| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.31 r_work: 0.2997 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25960 Z= 0.124 Angle : 0.576 9.622 35486 Z= 0.282 Chirality : 0.044 0.337 4236 Planarity : 0.004 0.047 4445 Dihedral : 5.577 56.300 5054 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 1.48 % Allowed : 16.10 % Favored : 82.42 % 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: 0.24 (0.15), residues: 3041 helix: 2.45 (0.21), residues: 657 sheet: 0.74 (0.19), residues: 702 loop : -1.09 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1037 TYR 0.018 0.001 TYR C1065 PHE 0.024 0.001 PHE C 133 TRP 0.018 0.001 TRP C 64 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00290 (25837) covalent geometry : angle 0.55218 (35157) SS BOND : bond 0.00295 ( 40) SS BOND : angle 1.42537 ( 80) hydrogen bonds : bond 0.04995 ( 989) hydrogen bonds : angle 4.57118 ( 2712) link_BETA1-4 : bond 0.00385 ( 35) link_BETA1-4 : angle 1.83019 ( 105) link_NAG-ASN : bond 0.00294 ( 48) link_NAG-ASN : angle 1.93991 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7490.98 seconds wall clock time: 128 minutes 29.57 seconds (7709.57 seconds total)