Starting phenix.real_space_refine on Thu Mar 5 23:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v78_31762/03_2026/7v78_31762.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v78_31762/03_2026/7v78_31762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v78_31762/03_2026/7v78_31762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v78_31762/03_2026/7v78_31762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v78_31762/03_2026/7v78_31762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v78_31762/03_2026/7v78_31762.map" } resolution = 3.4 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= 0.059 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 111 5.16 5 C 16340 2.51 5 N 4134 2.21 5 O 5092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25677 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8152 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 7 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8158 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.72, per 1000 atoms: 0.22 Number of scatterers: 25677 At special positions: 0 Unit cell: (144.1, 151.8, 196.9, 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 111 16.00 O 5092 8.00 N 4134 7.00 C 16340 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 122 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG A2005 " - " ASN A 20 " " NAG A2006 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG B2007 " - " ASN B 188 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG C2006 " - " ASN C 188 " " NAG D 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " " NAG l 1 " - " ASN C 20 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 45 sheets defined 25.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.320A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.289A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.527A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.776A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.945A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.096A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.548A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.879A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.761A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.617A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.536A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.564A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.884A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.609A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.514A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.724A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.716A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.211A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.663A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.699A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.087A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.738A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.728A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.539A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 633 through 638 removed outlier: 3.989A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.752A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.507A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.731A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.968A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.984A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.440A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.006A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.541A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.555A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.012A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.825A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.034A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.611A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.756A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.934A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.060A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.746A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.396A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.412A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.654A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.047A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.369A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.260A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.055A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.574A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.581A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.010A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.620A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.026A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.811A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.605A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.514A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 659 removed outlier: 5.149A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.650A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.650A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.644A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1004 hydrogen bonds defined for protein. 2709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.40 Time building geometry restraints manager: 3.18 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: 8030 1.34 - 1.46: 6697 1.46 - 1.58: 11381 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 26246 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG A2001 " pdb=" O5 NAG A2001 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 26241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 35174 2.24 - 4.47: 510 4.47 - 6.71: 30 6.71 - 8.94: 6 8.94 - 11.18: 2 Bond angle restraints: 35722 Sorted by residual: angle pdb=" N VAL B1128 " pdb=" CA VAL B1128 " pdb=" C VAL B1128 " ideal model delta sigma weight residual 112.96 109.19 3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 107.88 112.94 -5.06 1.41e+00 5.03e-01 1.29e+01 angle pdb=" C CYS C 662 " pdb=" N ASP C 663 " pdb=" CA ASP C 663 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 angle pdb=" C VAL B 483 " pdb=" N LYS B 484 " pdb=" CA LYS B 484 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.89e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.50 -3.80 1.22e+00 6.72e-01 9.72e+00 ... (remaining 35717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.35: 15676 24.35 - 48.69: 830 48.69 - 73.04: 134 73.04 - 97.39: 55 97.39 - 121.73: 59 Dihedral angle restraints: 16754 sinusoidal: 7661 harmonic: 9093 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 7.06 85.94 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -168.85 82.85 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -167.29 81.29 1 1.00e+01 1.00e-02 8.15e+01 ... (remaining 16751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4233 0.116 - 0.232: 65 0.232 - 0.348: 4 0.348 - 0.464: 5 0.464 - 0.580: 1 Chirality restraints: 4308 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 4305 not shown) Planarity restraints: 4543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A 986 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO A 987 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.018 2.00e-02 2.50e+03 1.59e-02 4.40e+00 pdb=" CG PHE C 906 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.003 2.00e-02 2.50e+03 ... (remaining 4540 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 703 2.69 - 3.25: 24655 3.25 - 3.80: 38050 3.80 - 4.35: 47188 4.35 - 4.90: 82070 Nonbonded interactions: 192666 Sorted by model distance: nonbonded pdb=" OD1 ASN A 125 " pdb=" O3 NAG A2002 " model vdw 2.142 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.191 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.193 3.040 nonbonded pdb=" OE2 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.217 3.120 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.225 3.040 ... (remaining 192661 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 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) selection = (chain 'C' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) } ncs_group { reference = chain 'D' 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: 5.780 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.090 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26375 Z= 0.216 Angle : 0.667 12.375 36066 Z= 0.321 Chirality : 0.049 0.580 4308 Planarity : 0.004 0.070 4491 Dihedral : 16.532 121.733 10790 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.47 % 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: -0.20 (0.15), residues: 3075 helix: 1.76 (0.21), residues: 665 sheet: 0.20 (0.18), residues: 766 loop : -1.12 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.014 0.001 TYR A1067 PHE 0.037 0.001 PHE C 906 TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00458 (26246) covalent geometry : angle 0.62903 (35722) SS BOND : bond 0.00373 ( 40) SS BOND : angle 1.61785 ( 80) hydrogen bonds : bond 0.12860 ( 992) hydrogen bonds : angle 5.99379 ( 2709) Misc. bond : bond 0.00019 ( 1) link_BETA1-4 : bond 0.00374 ( 36) link_BETA1-4 : angle 1.81934 ( 108) link_NAG-ASN : bond 0.00470 ( 52) link_NAG-ASN : angle 2.95573 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7736 (p0) cc_final: 0.7470 (p0) REVERT: A 153 MET cc_start: 0.7178 (pmm) cc_final: 0.5009 (mtm) REVERT: A 242 LEU cc_start: 0.8297 (mm) cc_final: 0.8070 (mm) REVERT: A 334 ASN cc_start: 0.8599 (t0) cc_final: 0.8335 (t0) REVERT: B 138 TYR cc_start: 0.8330 (t80) cc_final: 0.8102 (t80) REVERT: B 140 PHE cc_start: 0.7625 (p90) cc_final: 0.6449 (p90) REVERT: B 153 MET cc_start: 0.5556 (ppp) cc_final: 0.3645 (pmm) REVERT: B 197 ILE cc_start: 0.7955 (mt) cc_final: 0.7233 (mt) REVERT: B 389 ASP cc_start: 0.8771 (m-30) cc_final: 0.8154 (t0) REVERT: B 900 MET cc_start: 0.7939 (mtt) cc_final: 0.7673 (mtp) REVERT: B 902 MET cc_start: 0.8067 (mmm) cc_final: 0.7743 (mmt) REVERT: B 1132 ILE cc_start: 0.8371 (pt) cc_final: 0.8156 (pt) REVERT: C 140 PHE cc_start: 0.7861 (p90) cc_final: 0.7588 (p90) REVERT: C 198 ASP cc_start: 0.8166 (m-30) cc_final: 0.7792 (m-30) REVERT: C 239 GLN cc_start: 0.7325 (tt0) cc_final: 0.7038 (tt0) REVERT: C 498 GLN cc_start: 0.7890 (mm110) cc_final: 0.7483 (mm-40) REVERT: C 773 GLU cc_start: 0.7467 (tt0) cc_final: 0.7251 (tt0) REVERT: C 990 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8062 (mm-30) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1418 time to fit residues: 55.5391 Evaluate side-chains 170 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN B1010 GLN C 196 ASN C 394 ASN C 774 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104380 restraints weight = 39387.980| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.25 r_work: 0.3295 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26375 Z= 0.188 Angle : 0.669 10.757 36066 Z= 0.322 Chirality : 0.050 0.399 4308 Planarity : 0.004 0.065 4491 Dihedral : 12.957 105.974 5241 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.89 % Rotamer: Outliers : 0.73 % Allowed : 6.82 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3075 helix: 1.67 (0.21), residues: 661 sheet: 0.12 (0.18), residues: 758 loop : -1.20 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.020 0.001 TYR A1067 PHE 0.028 0.002 PHE C 906 TRP 0.016 0.001 TRP A 436 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00458 (26246) covalent geometry : angle 0.63319 (35722) SS BOND : bond 0.00422 ( 40) SS BOND : angle 1.68282 ( 80) hydrogen bonds : bond 0.05782 ( 992) hydrogen bonds : angle 5.12685 ( 2709) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00439 ( 36) link_BETA1-4 : angle 1.81364 ( 108) link_NAG-ASN : bond 0.00450 ( 52) link_NAG-ASN : angle 2.81615 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7182 (pmm) cc_final: 0.5076 (mtm) REVERT: A 334 ASN cc_start: 0.8799 (t0) cc_final: 0.8543 (t0) REVERT: A 988 GLU cc_start: 0.8123 (mp0) cc_final: 0.7841 (mp0) REVERT: B 138 TYR cc_start: 0.8500 (t80) cc_final: 0.8098 (t80) REVERT: B 140 PHE cc_start: 0.7494 (p90) cc_final: 0.6446 (p90) REVERT: B 153 MET cc_start: 0.5009 (ppp) cc_final: 0.2974 (pmm) REVERT: B 197 ILE cc_start: 0.8133 (mt) cc_final: 0.7891 (mt) REVERT: B 389 ASP cc_start: 0.8640 (m-30) cc_final: 0.8205 (t0) REVERT: B 1029 MET cc_start: 0.9135 (tpp) cc_final: 0.8731 (ttm) REVERT: C 498 GLN cc_start: 0.8088 (mm110) cc_final: 0.7552 (mm-40) REVERT: C 950 ASP cc_start: 0.8331 (t70) cc_final: 0.8046 (t0) REVERT: C 1029 MET cc_start: 0.8908 (tpp) cc_final: 0.8391 (ttt) outliers start: 20 outliers final: 14 residues processed: 197 average time/residue: 0.1494 time to fit residues: 48.5921 Evaluate side-chains 174 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 84 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 245 HIS C 493 GLN C 498 GLN C 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.150900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.096935 restraints weight = 39374.085| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.46 r_work: 0.3064 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26375 Z= 0.194 Angle : 0.674 14.158 36066 Z= 0.323 Chirality : 0.049 0.380 4308 Planarity : 0.004 0.057 4491 Dihedral : 11.559 101.044 5241 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.89 % Rotamer: Outliers : 1.28 % Allowed : 10.01 % Favored : 88.71 % 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: -0.42 (0.15), residues: 3075 helix: 1.57 (0.21), residues: 659 sheet: 0.09 (0.18), residues: 763 loop : -1.26 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1039 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.002 PHE C 238 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00473 (26246) covalent geometry : angle 0.62711 (35722) SS BOND : bond 0.00379 ( 40) SS BOND : angle 1.59734 ( 80) hydrogen bonds : bond 0.05885 ( 992) hydrogen bonds : angle 5.05199 ( 2709) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00471 ( 36) link_BETA1-4 : angle 1.89720 ( 108) link_NAG-ASN : bond 0.00453 ( 52) link_NAG-ASN : angle 3.34782 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7163 (pmm) cc_final: 0.5154 (mtm) REVERT: A 334 ASN cc_start: 0.8786 (t0) cc_final: 0.8528 (t0) REVERT: A 436 TRP cc_start: 0.6889 (p90) cc_final: 0.6570 (p90) REVERT: A 988 GLU cc_start: 0.8100 (mp0) cc_final: 0.7795 (mp0) REVERT: A 1132 ILE cc_start: 0.8790 (pt) cc_final: 0.8505 (pt) REVERT: B 138 TYR cc_start: 0.8481 (t80) cc_final: 0.8146 (t80) REVERT: B 140 PHE cc_start: 0.7494 (p90) cc_final: 0.6411 (p90) REVERT: B 153 MET cc_start: 0.5148 (ppp) cc_final: 0.3150 (pmm) REVERT: B 957 GLN cc_start: 0.9030 (tt0) cc_final: 0.8567 (tm-30) REVERT: B 1029 MET cc_start: 0.8969 (tpp) cc_final: 0.8767 (ttm) REVERT: C 200 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7310 (t80) REVERT: C 498 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7485 (mm-40) REVERT: C 950 ASP cc_start: 0.8538 (t70) cc_final: 0.8188 (t0) outliers start: 35 outliers final: 22 residues processed: 192 average time/residue: 0.1456 time to fit residues: 46.3338 Evaluate side-chains 178 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 114 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 252 optimal weight: 9.9990 chunk 16 optimal weight: 0.0470 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN B 239 GLN B1106 GLN C 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.152846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099079 restraints weight = 39004.645| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.27 r_work: 0.3096 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26375 Z= 0.127 Angle : 0.621 14.045 36066 Z= 0.294 Chirality : 0.047 0.374 4308 Planarity : 0.004 0.054 4491 Dihedral : 10.263 96.231 5241 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 1.91 % Allowed : 11.22 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3075 helix: 1.75 (0.21), residues: 657 sheet: 0.20 (0.19), residues: 748 loop : -1.19 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.019 0.001 TYR B 351 PHE 0.025 0.001 PHE A 133 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00287 (26246) covalent geometry : angle 0.57169 (35722) SS BOND : bond 0.00311 ( 40) SS BOND : angle 1.36596 ( 80) hydrogen bonds : bond 0.05086 ( 992) hydrogen bonds : angle 4.81709 ( 2709) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00510 ( 36) link_BETA1-4 : angle 1.94881 ( 108) link_NAG-ASN : bond 0.00621 ( 52) link_NAG-ASN : angle 3.27484 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8403 (p90) cc_final: 0.8172 (p90) REVERT: A 153 MET cc_start: 0.7128 (pmm) cc_final: 0.5170 (mtm) REVERT: A 334 ASN cc_start: 0.8844 (t0) cc_final: 0.8599 (t0) REVERT: A 436 TRP cc_start: 0.7098 (p90) cc_final: 0.6742 (p90) REVERT: A 563 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 1132 ILE cc_start: 0.8636 (pt) cc_final: 0.8361 (pt) REVERT: B 134 GLN cc_start: 0.8317 (mm110) cc_final: 0.7956 (mm110) REVERT: B 140 PHE cc_start: 0.7573 (p90) cc_final: 0.6310 (p90) REVERT: B 153 MET cc_start: 0.5062 (ppp) cc_final: 0.3199 (pmm) REVERT: B 448 ASN cc_start: 0.7199 (t0) cc_final: 0.6885 (t0) REVERT: B 451 TYR cc_start: 0.7420 (m-80) cc_final: 0.7169 (m-80) REVERT: B 950 ASP cc_start: 0.8640 (m-30) cc_final: 0.8306 (m-30) REVERT: B 957 GLN cc_start: 0.9027 (tt0) cc_final: 0.8580 (tm-30) REVERT: B 1029 MET cc_start: 0.8909 (tpp) cc_final: 0.8513 (ttm) REVERT: C 140 PHE cc_start: 0.7874 (p90) cc_final: 0.7591 (p90) REVERT: C 200 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7261 (t80) REVERT: C 462 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7829 (mmmm) REVERT: C 498 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7668 (mm-40) REVERT: C 1029 MET cc_start: 0.8692 (tpp) cc_final: 0.8190 (ttm) outliers start: 52 outliers final: 25 residues processed: 215 average time/residue: 0.1418 time to fit residues: 50.9616 Evaluate side-chains 193 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 65 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 303 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 308 optimal weight: 0.4980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 239 GLN C 245 HIS C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.150922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097169 restraints weight = 38949.850| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.42 r_work: 0.3064 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26375 Z= 0.180 Angle : 0.658 13.163 36066 Z= 0.315 Chirality : 0.048 0.371 4308 Planarity : 0.004 0.056 4491 Dihedral : 9.746 95.758 5241 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 2.16 % Allowed : 12.43 % Favored : 85.41 % 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: -0.36 (0.15), residues: 3075 helix: 1.60 (0.21), residues: 659 sheet: 0.12 (0.19), residues: 761 loop : -1.22 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 214 TYR 0.019 0.001 TYR B 351 PHE 0.020 0.002 PHE B1121 TRP 0.018 0.001 TRP A 353 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00433 (26246) covalent geometry : angle 0.61190 (35722) SS BOND : bond 0.00412 ( 40) SS BOND : angle 1.54897 ( 80) hydrogen bonds : bond 0.05729 ( 992) hydrogen bonds : angle 4.90336 ( 2709) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00481 ( 36) link_BETA1-4 : angle 1.90405 ( 108) link_NAG-ASN : bond 0.00533 ( 52) link_NAG-ASN : angle 3.26318 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7158 (pmm) cc_final: 0.5224 (mtm) REVERT: A 334 ASN cc_start: 0.8865 (t0) cc_final: 0.8645 (t0) REVERT: A 436 TRP cc_start: 0.7064 (p90) cc_final: 0.6766 (p90) REVERT: A 563 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: B 140 PHE cc_start: 0.7472 (p90) cc_final: 0.6201 (p90) REVERT: B 153 MET cc_start: 0.4892 (ppp) cc_final: 0.2554 (pmm) REVERT: B 895 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: B 957 GLN cc_start: 0.9013 (tt0) cc_final: 0.8552 (tm-30) REVERT: B 1029 MET cc_start: 0.8955 (tpp) cc_final: 0.8559 (ttm) REVERT: C 158 ARG cc_start: 0.6229 (ptm160) cc_final: 0.5927 (ptm160) REVERT: C 200 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7255 (t80) REVERT: C 462 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7841 (mmmm) REVERT: C 498 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7999 (mm-40) outliers start: 59 outliers final: 37 residues processed: 215 average time/residue: 0.1473 time to fit residues: 52.8509 Evaluate side-chains 203 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 254 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 239 GLN C 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094938 restraints weight = 39454.795| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.52 r_work: 0.3026 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 26375 Z= 0.235 Angle : 0.701 12.164 36066 Z= 0.340 Chirality : 0.050 0.364 4308 Planarity : 0.004 0.052 4491 Dihedral : 9.219 94.174 5241 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 2.79 % Allowed : 13.24 % Favored : 83.98 % 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: -0.56 (0.15), residues: 3075 helix: 1.43 (0.21), residues: 658 sheet: 0.02 (0.19), residues: 753 loop : -1.35 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.021 0.001 TYR A1067 PHE 0.023 0.002 PHE C 543 TRP 0.019 0.001 TRP A 353 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00579 (26246) covalent geometry : angle 0.65606 (35722) SS BOND : bond 0.00476 ( 40) SS BOND : angle 1.75138 ( 80) hydrogen bonds : bond 0.06402 ( 992) hydrogen bonds : angle 5.06051 ( 2709) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00454 ( 36) link_BETA1-4 : angle 1.89923 ( 108) link_NAG-ASN : bond 0.00526 ( 52) link_NAG-ASN : angle 3.32056 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 171 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7170 (pmm) cc_final: 0.5115 (mtm) REVERT: A 334 ASN cc_start: 0.8857 (t0) cc_final: 0.8595 (t0) REVERT: A 436 TRP cc_start: 0.6927 (p90) cc_final: 0.6724 (p90) REVERT: A 563 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: B 114 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8224 (p) REVERT: B 140 PHE cc_start: 0.7511 (p90) cc_final: 0.6208 (p90) REVERT: B 153 MET cc_start: 0.4824 (ppp) cc_final: 0.2589 (pmm) REVERT: B 353 TRP cc_start: 0.7436 (p-90) cc_final: 0.7089 (p-90) REVERT: B 895 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: B 957 GLN cc_start: 0.9053 (tt0) cc_final: 0.8599 (tm-30) REVERT: B 1029 MET cc_start: 0.8946 (tpp) cc_final: 0.8491 (ttm) REVERT: C 140 PHE cc_start: 0.7633 (p90) cc_final: 0.7217 (p90) REVERT: C 200 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7306 (t80) REVERT: C 383 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8718 (m) REVERT: C 498 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8019 (mm-40) REVERT: C 661 GLU cc_start: 0.8108 (tp30) cc_final: 0.7363 (mp0) outliers start: 76 outliers final: 45 residues processed: 231 average time/residue: 0.1476 time to fit residues: 57.3111 Evaluate side-chains 213 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 116 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 197 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 150 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.149648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089111 restraints weight = 39029.204| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.26 r_work: 0.3015 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26375 Z= 0.115 Angle : 0.608 11.385 36066 Z= 0.293 Chirality : 0.047 0.375 4308 Planarity : 0.004 0.051 4491 Dihedral : 8.611 90.074 5241 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.61 % Allowed : 14.81 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3075 helix: 1.77 (0.21), residues: 656 sheet: 0.18 (0.19), residues: 734 loop : -1.20 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.001 PHE B 168 TRP 0.019 0.001 TRP A 353 HIS 0.002 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00247 (26246) covalent geometry : angle 0.56482 (35722) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.37774 ( 80) hydrogen bonds : bond 0.04957 ( 992) hydrogen bonds : angle 4.75258 ( 2709) Misc. bond : bond 0.00003 ( 1) link_BETA1-4 : bond 0.00520 ( 36) link_BETA1-4 : angle 1.99365 ( 108) link_NAG-ASN : bond 0.00563 ( 52) link_NAG-ASN : angle 2.95802 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7232 (pmm) cc_final: 0.5103 (mtm) REVERT: A 334 ASN cc_start: 0.8846 (t0) cc_final: 0.8582 (t0) REVERT: A 436 TRP cc_start: 0.7168 (p90) cc_final: 0.6875 (p90) REVERT: A 563 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: A 957 GLN cc_start: 0.8443 (tt0) cc_final: 0.8185 (tt0) REVERT: B 114 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 134 GLN cc_start: 0.8280 (mm110) cc_final: 0.7944 (mm110) REVERT: B 140 PHE cc_start: 0.7473 (p90) cc_final: 0.6139 (p90) REVERT: B 153 MET cc_start: 0.4826 (ppp) cc_final: 0.2556 (pmm) REVERT: B 353 TRP cc_start: 0.7306 (p-90) cc_final: 0.7003 (p-90) REVERT: B 895 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: B 957 GLN cc_start: 0.9042 (tt0) cc_final: 0.8539 (tm-30) REVERT: B 1029 MET cc_start: 0.8787 (tpp) cc_final: 0.8414 (ttm) REVERT: B 1039 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8554 (mtp180) REVERT: C 200 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7249 (t80) REVERT: C 383 SER cc_start: 0.8795 (t) cc_final: 0.8485 (m) REVERT: C 462 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7833 (mmmm) REVERT: C 498 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7896 (mm-40) REVERT: C 569 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6979 (mp) REVERT: C 661 GLU cc_start: 0.7837 (tp30) cc_final: 0.7051 (mp0) outliers start: 44 outliers final: 23 residues processed: 218 average time/residue: 0.1547 time to fit residues: 55.5660 Evaluate side-chains 203 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 0.0270 chunk 184 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 239 GLN C 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.149038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088385 restraints weight = 39145.839| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.25 r_work: 0.3001 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26375 Z= 0.133 Angle : 0.614 10.464 36066 Z= 0.296 Chirality : 0.047 0.368 4308 Planarity : 0.004 0.050 4491 Dihedral : 8.369 89.250 5241 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 1.65 % Allowed : 14.74 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3075 helix: 1.73 (0.21), residues: 664 sheet: 0.16 (0.19), residues: 752 loop : -1.19 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 214 TYR 0.017 0.001 TYR A1067 PHE 0.021 0.001 PHE A 133 TRP 0.020 0.001 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00306 (26246) covalent geometry : angle 0.57247 (35722) SS BOND : bond 0.00348 ( 40) SS BOND : angle 1.37374 ( 80) hydrogen bonds : bond 0.05101 ( 992) hydrogen bonds : angle 4.72656 ( 2709) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00512 ( 36) link_BETA1-4 : angle 1.98254 ( 108) link_NAG-ASN : bond 0.00515 ( 52) link_NAG-ASN : angle 2.92492 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7221 (pmm) cc_final: 0.5093 (mtm) REVERT: A 214 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6819 (tmm160) REVERT: A 334 ASN cc_start: 0.8828 (t0) cc_final: 0.8560 (t0) REVERT: A 436 TRP cc_start: 0.7128 (p90) cc_final: 0.6846 (p90) REVERT: A 563 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: B 114 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 134 GLN cc_start: 0.8318 (mm110) cc_final: 0.7964 (mm110) REVERT: B 140 PHE cc_start: 0.7465 (p90) cc_final: 0.6131 (p90) REVERT: B 153 MET cc_start: 0.4887 (ppp) cc_final: 0.2634 (pmm) REVERT: B 353 TRP cc_start: 0.7286 (p-90) cc_final: 0.6995 (p-90) REVERT: B 448 ASN cc_start: 0.7189 (t0) cc_final: 0.6784 (t0) REVERT: B 895 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: B 957 GLN cc_start: 0.9042 (tt0) cc_final: 0.8531 (tm-30) REVERT: B 1029 MET cc_start: 0.8812 (tpp) cc_final: 0.8420 (ttm) REVERT: B 1039 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8592 (mtp180) REVERT: C 200 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7219 (t80) REVERT: C 383 SER cc_start: 0.8688 (t) cc_final: 0.8455 (m) REVERT: C 462 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7834 (mmmm) REVERT: C 493 GLN cc_start: 0.6829 (mm110) cc_final: 0.6526 (mm-40) REVERT: C 775 ASP cc_start: 0.8264 (t0) cc_final: 0.8018 (m-30) outliers start: 45 outliers final: 34 residues processed: 208 average time/residue: 0.1477 time to fit residues: 50.7513 Evaluate side-chains 208 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 270 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 4.9990 chunk 239 optimal weight: 0.3980 chunk 279 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 304 optimal weight: 0.8980 chunk 309 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099544 restraints weight = 39186.821| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.56 r_work: 0.3142 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26375 Z= 0.117 Angle : 0.597 9.721 36066 Z= 0.287 Chirality : 0.047 0.368 4308 Planarity : 0.004 0.047 4491 Dihedral : 8.061 86.947 5241 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 1.72 % Allowed : 14.85 % Favored : 83.43 % 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: 3075 helix: 1.89 (0.21), residues: 654 sheet: 0.25 (0.19), residues: 732 loop : -1.13 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 214 TYR 0.017 0.001 TYR A1067 PHE 0.017 0.001 PHE B1121 TRP 0.020 0.001 TRP A 353 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00261 (26246) covalent geometry : angle 0.55574 (35722) SS BOND : bond 0.00304 ( 40) SS BOND : angle 1.24043 ( 80) hydrogen bonds : bond 0.04694 ( 992) hydrogen bonds : angle 4.64837 ( 2709) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00522 ( 36) link_BETA1-4 : angle 2.02032 ( 108) link_NAG-ASN : bond 0.00525 ( 52) link_NAG-ASN : angle 2.81561 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7168 (pmm) cc_final: 0.4849 (mtm) REVERT: A 334 ASN cc_start: 0.8814 (t0) cc_final: 0.8540 (t0) REVERT: A 436 TRP cc_start: 0.7094 (p90) cc_final: 0.6811 (p90) REVERT: A 563 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: A 957 GLN cc_start: 0.8438 (tt0) cc_final: 0.8200 (tt0) REVERT: B 114 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 134 GLN cc_start: 0.8311 (mm110) cc_final: 0.7958 (mm110) REVERT: B 140 PHE cc_start: 0.7498 (p90) cc_final: 0.6151 (p90) REVERT: B 153 MET cc_start: 0.4829 (ppp) cc_final: 0.2573 (pmm) REVERT: B 353 TRP cc_start: 0.7237 (p-90) cc_final: 0.6985 (p-90) REVERT: B 448 ASN cc_start: 0.7182 (t0) cc_final: 0.6782 (t0) REVERT: B 895 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: B 950 ASP cc_start: 0.8688 (m-30) cc_final: 0.8322 (m-30) REVERT: B 957 GLN cc_start: 0.9025 (tt0) cc_final: 0.8570 (tm-30) REVERT: B 1029 MET cc_start: 0.8880 (tpp) cc_final: 0.8512 (ttm) REVERT: B 1039 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8634 (mtp180) REVERT: C 140 PHE cc_start: 0.7476 (p90) cc_final: 0.7199 (p90) REVERT: C 200 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 383 SER cc_start: 0.8689 (t) cc_final: 0.8444 (m) REVERT: C 462 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7896 (mmmm) REVERT: C 493 GLN cc_start: 0.6855 (mm110) cc_final: 0.6551 (mm-40) REVERT: C 498 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7865 (mm-40) REVERT: C 569 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7030 (mp) REVERT: C 643 PHE cc_start: 0.7732 (t80) cc_final: 0.7353 (t80) REVERT: C 918 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: C 1029 MET cc_start: 0.8615 (tpp) cc_final: 0.8193 (ttt) outliers start: 47 outliers final: 33 residues processed: 213 average time/residue: 0.1539 time to fit residues: 54.0159 Evaluate side-chains 213 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 214 optimal weight: 0.4980 chunk 273 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 239 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.152837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099269 restraints weight = 39069.234| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.53 r_work: 0.3132 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26375 Z= 0.130 Angle : 0.607 9.632 36066 Z= 0.292 Chirality : 0.047 0.365 4308 Planarity : 0.004 0.048 4491 Dihedral : 7.993 85.759 5241 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.25 % Rotamer: Outliers : 1.76 % Allowed : 15.00 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3075 helix: 1.84 (0.21), residues: 657 sheet: 0.21 (0.19), residues: 753 loop : -1.11 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 214 TYR 0.017 0.001 TYR A1067 PHE 0.021 0.001 PHE A 133 TRP 0.020 0.001 TRP A 353 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00300 (26246) covalent geometry : angle 0.56667 (35722) SS BOND : bond 0.00304 ( 40) SS BOND : angle 1.40061 ( 80) hydrogen bonds : bond 0.04849 ( 992) hydrogen bonds : angle 4.65132 ( 2709) Misc. bond : bond 0.00005 ( 1) link_BETA1-4 : bond 0.00505 ( 36) link_BETA1-4 : angle 1.98541 ( 108) link_NAG-ASN : bond 0.00500 ( 52) link_NAG-ASN : angle 2.80484 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7163 (pmm) cc_final: 0.4849 (mtm) REVERT: A 334 ASN cc_start: 0.8806 (t0) cc_final: 0.8531 (t0) REVERT: A 436 TRP cc_start: 0.7092 (p90) cc_final: 0.6886 (p90) REVERT: A 563 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: A 1132 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8396 (pt) REVERT: B 114 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 134 GLN cc_start: 0.8330 (mm110) cc_final: 0.7967 (mm110) REVERT: B 140 PHE cc_start: 0.7441 (p90) cc_final: 0.6093 (p90) REVERT: B 153 MET cc_start: 0.4857 (ppp) cc_final: 0.2610 (pmm) REVERT: B 353 TRP cc_start: 0.7140 (p-90) cc_final: 0.6907 (p-90) REVERT: B 448 ASN cc_start: 0.7211 (t0) cc_final: 0.6807 (t0) REVERT: B 895 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: B 950 ASP cc_start: 0.8705 (m-30) cc_final: 0.8338 (m-30) REVERT: B 957 GLN cc_start: 0.9030 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 1029 MET cc_start: 0.8906 (tpp) cc_final: 0.8704 (ttm) REVERT: B 1039 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8621 (mtp180) REVERT: C 140 PHE cc_start: 0.7525 (p90) cc_final: 0.7155 (p90) REVERT: C 200 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.7200 (t80) REVERT: C 383 SER cc_start: 0.8673 (t) cc_final: 0.8431 (m) REVERT: C 462 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7913 (mmmm) REVERT: C 493 GLN cc_start: 0.6847 (mm110) cc_final: 0.6546 (mm-40) REVERT: C 498 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7812 (mm-40) REVERT: C 569 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7031 (mp) REVERT: C 918 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: C 1029 MET cc_start: 0.8576 (tpp) cc_final: 0.8169 (ttt) outliers start: 48 outliers final: 36 residues processed: 207 average time/residue: 0.1500 time to fit residues: 51.6752 Evaluate side-chains 211 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 102 optimal weight: 0.2980 chunk 222 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN B 239 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096826 restraints weight = 38987.540| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.58 r_work: 0.3052 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26375 Z= 0.194 Angle : 0.653 9.645 36066 Z= 0.318 Chirality : 0.049 0.359 4308 Planarity : 0.004 0.048 4491 Dihedral : 8.146 85.735 5241 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 1.94 % Allowed : 14.78 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3075 helix: 1.64 (0.21), residues: 661 sheet: 0.11 (0.19), residues: 751 loop : -1.23 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.020 0.001 TYR A1067 PHE 0.021 0.002 PHE B1121 TRP 0.020 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00475 (26246) covalent geometry : angle 0.61363 (35722) SS BOND : bond 0.00412 ( 40) SS BOND : angle 1.72314 ( 80) hydrogen bonds : bond 0.05761 ( 992) hydrogen bonds : angle 4.83641 ( 2709) Misc. bond : bond 0.00010 ( 1) link_BETA1-4 : bond 0.00490 ( 36) link_BETA1-4 : angle 1.94459 ( 108) link_NAG-ASN : bond 0.00466 ( 52) link_NAG-ASN : angle 2.88382 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5649.10 seconds wall clock time: 97 minutes 28.76 seconds (5848.76 seconds total)