Starting phenix.real_space_refine on Fri Mar 6 03:17:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbk_24981/03_2026/7sbk_24981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbk_24981/03_2026/7sbk_24981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sbk_24981/03_2026/7sbk_24981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbk_24981/03_2026/7sbk_24981.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbk_24981/03_2026/7sbk_24981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbk_24981/03_2026/7sbk_24981_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.042 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 117 5.16 5 C 17388 2.51 5 N 4416 2.21 5 O 5496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27417 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 8624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8624 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 52, 'TRANS': 1048} Chain breaks: 4 Chain: "A" Number of atoms: 8624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8624 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 52, 'TRANS': 1048} Chain breaks: 4 Chain: "C" Number of atoms: 8624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8624 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 52, 'TRANS': 1048} Chain breaks: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: "A" 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: 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 Time building chain proxies: 6.16, per 1000 atoms: 0.22 Number of scatterers: 27417 At special positions: 0 Unit cell: (143.562, 142.737, 193.066, 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 117 16.00 O 5496 8.00 N 4416 7.00 C 17388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG H 2 " - " MAN H 3 " " NAG I 2 " - " MAN I 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG Q 2 " - " MAN Q 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG a 2 " - " MAN a 3 " " NAG b 2 " - " MAN b 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG h 2 " - " MAN h 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG f 1 " - " FUC f 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN B 122 " " NAG E 1 " - " ASN B 234 " " NAG F 1 " - " ASN B 282 " " NAG G 1 " - " ASN B 616 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1074 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN A 122 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 282 " " NAG R 1 " - " ASN A 616 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A1074 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN A 343 " " NAG Y 1 " - " ASN A 165 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1074 " " NAG g 1 " - " ASN C1098 " " NAG h 1 " - " ASN C1134 " " NAG i 1 " - " ASN C 343 " " NAG j 1 " - " ASN C 165 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 27.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'B' and resid 154 through 160 removed outlier: 4.425A pdb=" N VAL B 159 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.929A pdb=" N ASN B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.633A pdb=" N ALA B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.556A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.745A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.042A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.891A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.797A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.607A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.112A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.206A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.425A pdb=" N VAL A 159 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.929A pdb=" N ASN A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.633A pdb=" N ALA A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.556A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.165A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.902A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.081A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.042A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.890A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.797A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.607A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.112A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.207A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1160 Processing helix chain 'C' and resid 154 through 160 removed outlier: 4.425A pdb=" N VAL C 159 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.928A pdb=" N ASN C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.633A pdb=" N ALA C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.557A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.165A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.102A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 618 through 624 removed outlier: 4.054A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.042A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (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: 3.890A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.797A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.608A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.112A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.208A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.482A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.540A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.699A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.860A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.138A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.370A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.088A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS A 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN B 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.950A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.482A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.700A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.859A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.138A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.370A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.088A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.714A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.950A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.482A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.699A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.860A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.137A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.088A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) 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 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.978A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.949A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 2967 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: 6.18 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4401 1.30 - 1.43: 7335 1.43 - 1.57: 16129 1.57 - 1.70: 2 1.70 - 1.83: 147 Bond restraints: 28014 Sorted by residual: bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.29e-02 6.01e+03 3.02e+01 bond pdb=" CA ARG B1019 " pdb=" C ARG B1019 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.37e-02 5.33e+03 2.71e+01 bond pdb=" N THR C 630 " pdb=" CA THR C 630 " ideal model delta sigma weight residual 1.461 1.505 -0.044 9.20e-03 1.18e+04 2.30e+01 bond pdb=" C4 NAG i 2 " pdb=" O4 NAG i 2 " ideal model delta sigma weight residual 1.409 1.490 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C4 NAG X 2 " pdb=" O4 NAG X 2 " ideal model delta sigma weight residual 1.409 1.490 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 28009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 33183 2.72 - 5.44: 4689 5.44 - 8.17: 217 8.17 - 10.89: 12 10.89 - 13.61: 2 Bond angle restraints: 38103 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 111.69 98.08 13.61 1.23e+00 6.61e-01 1.22e+02 angle pdb=" CA HIS A 625 " pdb=" CB HIS A 625 " pdb=" CG HIS A 625 " ideal model delta sigma weight residual 113.80 121.63 -7.83 1.00e+00 1.00e+00 6.14e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 112.54 103.06 9.48 1.22e+00 6.72e-01 6.04e+01 angle pdb=" CA HIS B 625 " pdb=" CB HIS B 625 " pdb=" CG HIS B 625 " ideal model delta sigma weight residual 113.80 121.11 -7.31 1.00e+00 1.00e+00 5.35e+01 angle pdb=" OD1 ASN C 149 " pdb=" CG ASN C 149 " pdb=" ND2 ASN C 149 " ideal model delta sigma weight residual 122.60 115.96 6.64 1.00e+00 1.00e+00 4.40e+01 ... (remaining 38098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.12: 17171 25.12 - 50.23: 689 50.23 - 75.35: 206 75.35 - 100.46: 39 100.46 - 125.58: 81 Dihedral angle restraints: 18186 sinusoidal: 8568 harmonic: 9618 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 18183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4405 0.195 - 0.389: 232 0.389 - 0.584: 9 0.584 - 0.778: 1 0.778 - 0.973: 3 Chirality restraints: 4650 Sorted by residual: chirality pdb=" C1 MAN L 3 " pdb=" O4 NAG L 2 " pdb=" C2 MAN L 3 " pdb=" O5 MAN L 3 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.39e+01 chirality pdb=" C1 MAN W 3 " pdb=" O4 NAG W 2 " pdb=" C2 MAN W 3 " pdb=" O5 MAN W 3 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.33e+01 chirality pdb=" C1 MAN h 3 " pdb=" O4 NAG h 2 " pdb=" C2 MAN h 3 " pdb=" O5 MAN h 3 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.29e+01 ... (remaining 4647 not shown) Planarity restraints: 4815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " 0.025 2.00e-02 2.50e+03 1.13e-01 1.60e+02 pdb=" CG ASN B 149 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " -0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG B1402 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " -0.025 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN C 149 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " 0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " -0.190 2.00e-02 2.50e+03 pdb=" C1 NAG C1402 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.025 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN A 149 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " -0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG A1402 " -0.128 2.00e-02 2.50e+03 ... (remaining 4812 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 1 2.05 - 2.76: 1763 2.76 - 3.48: 38752 3.48 - 4.19: 64316 4.19 - 4.90: 110146 Nonbonded interactions: 214978 Sorted by model distance: nonbonded pdb=" CG PRO C 295 " pdb=" CE1 TYR C 636 " model vdw 1.339 3.740 nonbonded pdb=" CG2 VAL C 608 " pdb=" OH TYR C 636 " model vdw 2.143 3.460 nonbonded pdb=" CG PRO C 295 " pdb=" CZ TYR C 636 " model vdw 2.202 3.660 nonbonded pdb=" OE1 GLU A 298 " pdb=" NE1 TRP A 633 " model vdw 2.209 3.120 nonbonded pdb=" OD2 ASP B 808 " pdb=" NZ LYS B 811 " model vdw 2.220 3.120 ... (remaining 214973 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'c' } 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: 7.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.680 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.015 0.081 28173 Z= 0.799 Angle : 1.838 18.025 38538 Z= 1.176 Chirality : 0.108 0.973 4650 Planarity : 0.012 0.088 4761 Dihedral : 17.410 125.578 11874 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.29 % Favored : 92.97 % Rotamer: Outliers : 1.49 % Allowed : 4.24 % Favored : 94.27 % Cbeta Deviations : 0.45 % 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: -1.92 (0.13), residues: 3273 helix: -1.42 (0.15), residues: 753 sheet: -0.18 (0.20), residues: 639 loop : -1.63 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 509 TYR 0.112 0.019 TYR C 145 PHE 0.095 0.015 PHE B 592 TRP 0.138 0.032 TRP B 258 HIS 0.028 0.004 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.01453 (28014) covalent geometry : angle 1.79210 (38103) SS BOND : bond 0.01161 ( 42) SS BOND : angle 2.84707 ( 84) hydrogen bonds : bond 0.18343 ( 1084) hydrogen bonds : angle 8.51327 ( 2967) link_ALPHA1-4 : bond 0.02634 ( 27) link_ALPHA1-4 : angle 3.79016 ( 81) link_BETA1-4 : bond 0.02499 ( 33) link_BETA1-4 : angle 3.87037 ( 99) link_BETA1-6 : bond 0.02987 ( 3) link_BETA1-6 : angle 2.15888 ( 9) link_NAG-ASN : bond 0.01164 ( 54) link_NAG-ASN : angle 5.26539 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 748 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 PHE cc_start: 0.7607 (p90) cc_final: 0.7260 (p90) REVERT: B 205 SER cc_start: 0.8675 (p) cc_final: 0.8363 (t) REVERT: B 208 THR cc_start: 0.8040 (m) cc_final: 0.7670 (p) REVERT: B 224 GLU cc_start: 0.7103 (mp0) cc_final: 0.6744 (mp0) REVERT: B 290 ASP cc_start: 0.7517 (t0) cc_final: 0.7301 (t0) REVERT: B 360 ASN cc_start: 0.8211 (t0) cc_final: 0.7889 (t0) REVERT: B 403 ARG cc_start: 0.7174 (ptm160) cc_final: 0.6965 (ptm160) REVERT: B 455 LEU cc_start: 0.8861 (tp) cc_final: 0.8346 (tp) REVERT: B 580 GLN cc_start: 0.7868 (mt0) cc_final: 0.7650 (mt0) REVERT: B 596 SER cc_start: 0.9062 (m) cc_final: 0.8740 (p) REVERT: B 610 VAL cc_start: 0.9116 (t) cc_final: 0.8826 (m) REVERT: B 642 VAL cc_start: 0.8993 (t) cc_final: 0.8732 (p) REVERT: B 820 ASP cc_start: 0.8005 (t0) cc_final: 0.7656 (t0) REVERT: B 823 PHE cc_start: 0.8348 (m-80) cc_final: 0.8121 (m-80) REVERT: B 850 ILE cc_start: 0.8135 (mp) cc_final: 0.7927 (pt) REVERT: B 902 MET cc_start: 0.8493 (mmm) cc_final: 0.8027 (tpt) REVERT: B 964 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8097 (mtpp) REVERT: B 967 SER cc_start: 0.8630 (m) cc_final: 0.8260 (p) REVERT: B 1050 MET cc_start: 0.8498 (ptp) cc_final: 0.8252 (ptp) REVERT: B 1127 ASP cc_start: 0.7702 (m-30) cc_final: 0.7483 (m-30) REVERT: B 1141 LEU cc_start: 0.8475 (tt) cc_final: 0.8057 (mm) REVERT: A 54 LEU cc_start: 0.8827 (mp) cc_final: 0.8447 (mt) REVERT: A 96 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.4769 (tt0) REVERT: A 129 LYS cc_start: 0.6894 (tttp) cc_final: 0.6661 (ttmm) REVERT: A 195 LYS cc_start: 0.8032 (tttt) cc_final: 0.7637 (tttt) REVERT: A 269 TYR cc_start: 0.6913 (m-80) cc_final: 0.6590 (m-80) REVERT: A 353 TRP cc_start: 0.8526 (p-90) cc_final: 0.8210 (p-90) REVERT: A 360 ASN cc_start: 0.8269 (t0) cc_final: 0.7927 (t0) REVERT: A 396 TYR cc_start: 0.7095 (m-10) cc_final: 0.6647 (m-10) REVERT: A 403 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6253 (ptm160) REVERT: A 453 TYR cc_start: 0.6188 (p90) cc_final: 0.5854 (p90) REVERT: A 455 LEU cc_start: 0.8720 (tp) cc_final: 0.8302 (tp) REVERT: A 596 SER cc_start: 0.9069 (m) cc_final: 0.8816 (p) REVERT: A 642 VAL cc_start: 0.9262 (t) cc_final: 0.8923 (p) REVERT: A 646 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7777 (tpt170) REVERT: A 823 PHE cc_start: 0.8267 (m-80) cc_final: 0.8037 (m-80) REVERT: A 850 ILE cc_start: 0.7994 (mp) cc_final: 0.7794 (pt) REVERT: A 926 GLN cc_start: 0.8718 (mt0) cc_final: 0.8488 (mt0) REVERT: A 986 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7921 (tttm) REVERT: A 990 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7008 (mt-10) REVERT: A 1017 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 1092 GLU cc_start: 0.7211 (pm20) cc_final: 0.6930 (pm20) REVERT: C 54 LEU cc_start: 0.8862 (mp) cc_final: 0.8509 (mp) REVERT: C 96 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5470 (tt0) REVERT: C 129 LYS cc_start: 0.6911 (tttp) cc_final: 0.6657 (tttt) REVERT: C 276 LEU cc_start: 0.8998 (tp) cc_final: 0.8789 (tp) REVERT: C 360 ASN cc_start: 0.8166 (t0) cc_final: 0.7964 (t0) REVERT: C 383 SER cc_start: 0.8892 (t) cc_final: 0.8679 (p) REVERT: C 402 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7586 (tp) REVERT: C 523 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7465 (p) REVERT: C 596 SER cc_start: 0.9060 (m) cc_final: 0.8647 (p) REVERT: C 642 VAL cc_start: 0.9130 (t) cc_final: 0.8818 (p) REVERT: C 661 GLU cc_start: 0.7746 (pm20) cc_final: 0.7471 (pm20) REVERT: C 697 MET cc_start: 0.8186 (ptm) cc_final: 0.7904 (ptm) REVERT: C 790 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8448 (mtmm) REVERT: C 902 MET cc_start: 0.8399 (mmm) cc_final: 0.8133 (mmt) REVERT: C 1037 SER cc_start: 0.9021 (t) cc_final: 0.8723 (p) REVERT: C 1041 ASP cc_start: 0.8042 (m-30) cc_final: 0.7796 (m-30) REVERT: C 1045 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8370 (tptp) REVERT: C 1125 ASN cc_start: 0.8360 (p0) cc_final: 0.8067 (p0) REVERT: C 1127 ASP cc_start: 0.7755 (m-30) cc_final: 0.7475 (m-30) outliers start: 43 outliers final: 8 residues processed: 773 average time/residue: 0.1919 time to fit residues: 227.0895 Evaluate side-chains 598 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 586 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 370 ASN B 751 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 777 ASN B 957 GLN B 969 ASN A 125 ASN A 317 ASN A 370 ASN A 450 ASN A 460 ASN A 777 ASN A 907 ASN A 957 GLN A 969 ASN A1119 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 460 ASN C 607 GLN C 751 ASN C 777 ASN C 907 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1119 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.113977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091490 restraints weight = 58489.608| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.36 r_work: 0.3266 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28173 Z= 0.182 Angle : 0.866 19.173 38538 Z= 0.417 Chirality : 0.052 0.749 4650 Planarity : 0.004 0.055 4761 Dihedral : 15.223 108.193 5955 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.52 % Favored : 95.26 % Rotamer: Outliers : 1.88 % Allowed : 9.44 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3273 helix: 0.86 (0.19), residues: 729 sheet: -0.12 (0.18), residues: 759 loop : -1.35 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 634 TYR 0.028 0.002 TYR A 495 PHE 0.028 0.002 PHE B 347 TRP 0.020 0.003 TRP B 258 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00401 (28014) covalent geometry : angle 0.80133 (38103) SS BOND : bond 0.00386 ( 42) SS BOND : angle 2.39998 ( 84) hydrogen bonds : bond 0.05289 ( 1084) hydrogen bonds : angle 6.41937 ( 2967) link_ALPHA1-4 : bond 0.01293 ( 27) link_ALPHA1-4 : angle 2.61027 ( 81) link_BETA1-4 : bond 0.00457 ( 33) link_BETA1-4 : angle 1.92248 ( 99) link_BETA1-6 : bond 0.01369 ( 3) link_BETA1-6 : angle 1.67775 ( 9) link_NAG-ASN : bond 0.00672 ( 54) link_NAG-ASN : angle 4.30014 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 632 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.8007 (m) cc_final: 0.7735 (m) REVERT: B 99 ASN cc_start: 0.8475 (t0) cc_final: 0.8164 (t0) REVERT: B 140 PHE cc_start: 0.7994 (p90) cc_final: 0.7658 (p90) REVERT: B 177 MET cc_start: 0.5227 (mpp) cc_final: 0.4883 (mmt) REVERT: B 360 ASN cc_start: 0.8463 (t0) cc_final: 0.8235 (t0) REVERT: B 460 ASN cc_start: 0.8328 (m-40) cc_final: 0.7818 (m110) REVERT: B 565 PHE cc_start: 0.7299 (m-10) cc_final: 0.6817 (m-10) REVERT: B 572 THR cc_start: 0.9015 (p) cc_final: 0.8087 (p) REVERT: B 596 SER cc_start: 0.9261 (m) cc_final: 0.8861 (p) REVERT: B 633 TRP cc_start: 0.8506 (p-90) cc_final: 0.7712 (p-90) REVERT: B 642 VAL cc_start: 0.9034 (t) cc_final: 0.8799 (p) REVERT: B 820 ASP cc_start: 0.8239 (t0) cc_final: 0.7896 (m-30) REVERT: B 990 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 1005 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: B 1017 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 1050 MET cc_start: 0.8627 (ptp) cc_final: 0.8271 (ptm) REVERT: B 1092 GLU cc_start: 0.7857 (pm20) cc_final: 0.7639 (pm20) REVERT: B 1107 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8208 (mtt90) REVERT: A 99 ASN cc_start: 0.8531 (t0) cc_final: 0.8229 (t0) REVERT: A 289 VAL cc_start: 0.8962 (t) cc_final: 0.8531 (m) REVERT: A 342 PHE cc_start: 0.8499 (m-80) cc_final: 0.8132 (m-80) REVERT: A 360 ASN cc_start: 0.8618 (t0) cc_final: 0.8208 (t0) REVERT: A 479 PRO cc_start: 0.6388 (Cg_endo) cc_final: 0.6175 (Cg_exo) REVERT: A 523 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7620 (p) REVERT: A 565 PHE cc_start: 0.7425 (m-10) cc_final: 0.6907 (m-10) REVERT: A 583 GLU cc_start: 0.8033 (pp20) cc_final: 0.7529 (pp20) REVERT: A 584 ILE cc_start: 0.9033 (mm) cc_final: 0.8736 (mm) REVERT: A 586 ASP cc_start: 0.8110 (t0) cc_final: 0.7862 (t0) REVERT: A 596 SER cc_start: 0.9322 (m) cc_final: 0.8867 (p) REVERT: A 633 TRP cc_start: 0.8501 (p-90) cc_final: 0.8262 (p-90) REVERT: A 725 GLU cc_start: 0.8472 (tt0) cc_final: 0.8201 (tt0) REVERT: A 773 GLU cc_start: 0.8442 (tt0) cc_final: 0.8205 (tt0) REVERT: A 790 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8756 (mtmm) REVERT: A 904 TYR cc_start: 0.8514 (m-10) cc_final: 0.8130 (m-10) REVERT: A 926 GLN cc_start: 0.8881 (mt0) cc_final: 0.8669 (mt0) REVERT: A 986 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8378 (ttmm) REVERT: A 990 GLU cc_start: 0.8202 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 1017 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 1092 GLU cc_start: 0.7781 (pm20) cc_final: 0.7562 (pm20) REVERT: C 84 LEU cc_start: 0.8214 (mt) cc_final: 0.7987 (mp) REVERT: C 99 ASN cc_start: 0.8417 (t0) cc_final: 0.8149 (t0) REVERT: C 177 MET cc_start: 0.5322 (mpp) cc_final: 0.5087 (mmt) REVERT: C 190 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7831 (mmt-90) REVERT: C 258 TRP cc_start: 0.5314 (m-10) cc_final: 0.5105 (m-10) REVERT: C 271 GLN cc_start: 0.8649 (mt0) cc_final: 0.8395 (mt0) REVERT: C 275 PHE cc_start: 0.8678 (m-80) cc_final: 0.8442 (m-80) REVERT: C 276 LEU cc_start: 0.9039 (tp) cc_final: 0.8783 (tt) REVERT: C 324 GLU cc_start: 0.7938 (pm20) cc_final: 0.7606 (pm20) REVERT: C 342 PHE cc_start: 0.8327 (m-80) cc_final: 0.8107 (m-80) REVERT: C 383 SER cc_start: 0.8993 (t) cc_final: 0.8681 (p) REVERT: C 434 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8595 (pt) REVERT: C 436 TRP cc_start: 0.6923 (p90) cc_final: 0.6575 (p90) REVERT: C 495 TYR cc_start: 0.6013 (m-80) cc_final: 0.5591 (m-80) REVERT: C 523 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7723 (p) REVERT: C 565 PHE cc_start: 0.7242 (m-10) cc_final: 0.6988 (m-10) REVERT: C 596 SER cc_start: 0.9251 (m) cc_final: 0.8716 (p) REVERT: C 610 VAL cc_start: 0.8976 (t) cc_final: 0.8697 (m) REVERT: C 646 ARG cc_start: 0.8538 (tpt-90) cc_final: 0.7995 (tpt170) REVERT: C 790 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8717 (mtmm) REVERT: C 820 ASP cc_start: 0.8397 (t0) cc_final: 0.7954 (m-30) REVERT: C 902 MET cc_start: 0.8682 (mmm) cc_final: 0.8354 (mmt) REVERT: C 1037 SER cc_start: 0.9177 (t) cc_final: 0.8844 (p) REVERT: C 1125 ASN cc_start: 0.8667 (p0) cc_final: 0.8455 (p0) outliers start: 54 outliers final: 28 residues processed: 661 average time/residue: 0.1865 time to fit residues: 192.3989 Evaluate side-chains 579 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 547 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 42 optimal weight: 0.0470 chunk 170 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 273 optimal weight: 0.0970 chunk 59 optimal weight: 0.3980 chunk 190 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 957 GLN B1002 GLN B1119 ASN A 751 ASN A 907 ASN C 360 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090900 restraints weight = 59257.476| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.32 r_work: 0.3259 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28173 Z= 0.171 Angle : 0.812 19.278 38538 Z= 0.383 Chirality : 0.050 0.725 4650 Planarity : 0.004 0.058 4761 Dihedral : 14.138 105.421 5953 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.65 % Rotamer: Outliers : 2.67 % Allowed : 11.70 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.66 (0.14), residues: 3273 helix: 1.22 (0.20), residues: 747 sheet: -0.06 (0.18), residues: 741 loop : -1.37 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 509 TYR 0.020 0.002 TYR C1067 PHE 0.025 0.002 PHE B1148 TRP 0.019 0.002 TRP C 353 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00388 (28014) covalent geometry : angle 0.75614 (38103) SS BOND : bond 0.00621 ( 42) SS BOND : angle 2.29975 ( 84) hydrogen bonds : bond 0.04647 ( 1084) hydrogen bonds : angle 6.14941 ( 2967) link_ALPHA1-4 : bond 0.01397 ( 27) link_ALPHA1-4 : angle 2.71293 ( 81) link_BETA1-4 : bond 0.00457 ( 33) link_BETA1-4 : angle 1.53867 ( 99) link_BETA1-6 : bond 0.01492 ( 3) link_BETA1-6 : angle 2.02975 ( 9) link_NAG-ASN : bond 0.00616 ( 54) link_NAG-ASN : angle 3.77734 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 592 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7974 (m) cc_final: 0.7725 (m) REVERT: B 99 ASN cc_start: 0.8382 (t0) cc_final: 0.8092 (t0) REVERT: B 140 PHE cc_start: 0.7917 (p90) cc_final: 0.7579 (p90) REVERT: B 360 ASN cc_start: 0.8436 (t0) cc_final: 0.8148 (t0) REVERT: B 436 TRP cc_start: 0.7144 (p90) cc_final: 0.6807 (p90) REVERT: B 452 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7710 (ptm160) REVERT: B 460 ASN cc_start: 0.8154 (m-40) cc_final: 0.7934 (m110) REVERT: B 523 THR cc_start: 0.8562 (m) cc_final: 0.8004 (p) REVERT: B 557 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8399 (ptmt) REVERT: B 565 PHE cc_start: 0.7272 (m-10) cc_final: 0.6776 (m-10) REVERT: B 596 SER cc_start: 0.9225 (m) cc_final: 0.8765 (p) REVERT: B 633 TRP cc_start: 0.8502 (p-90) cc_final: 0.8032 (p-90) REVERT: B 642 VAL cc_start: 0.9171 (t) cc_final: 0.8896 (p) REVERT: B 646 ARG cc_start: 0.8813 (tpt170) cc_final: 0.8494 (tpt170) REVERT: B 776 LYS cc_start: 0.8757 (tptm) cc_final: 0.8313 (ttpt) REVERT: B 808 ASP cc_start: 0.7638 (t0) cc_final: 0.7419 (t0) REVERT: B 815 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8579 (ttm110) REVERT: B 820 ASP cc_start: 0.8114 (t0) cc_final: 0.7817 (m-30) REVERT: B 990 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 1050 MET cc_start: 0.8656 (ptp) cc_final: 0.8327 (ptm) REVERT: B 1092 GLU cc_start: 0.7889 (pm20) cc_final: 0.7688 (pm20) REVERT: B 1107 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8246 (mtt90) REVERT: A 99 ASN cc_start: 0.8466 (t0) cc_final: 0.8210 (t0) REVERT: A 104 TRP cc_start: 0.7753 (m-90) cc_final: 0.7512 (m-90) REVERT: A 289 VAL cc_start: 0.8986 (t) cc_final: 0.8608 (m) REVERT: A 342 PHE cc_start: 0.8604 (m-80) cc_final: 0.8232 (m-80) REVERT: A 360 ASN cc_start: 0.8573 (t0) cc_final: 0.8143 (t0) REVERT: A 495 TYR cc_start: 0.5603 (m-80) cc_final: 0.5353 (m-80) REVERT: A 523 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 533 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8601 (pp) REVERT: A 565 PHE cc_start: 0.7379 (m-10) cc_final: 0.6858 (m-10) REVERT: A 583 GLU cc_start: 0.7940 (pp20) cc_final: 0.7592 (pp20) REVERT: A 584 ILE cc_start: 0.9028 (mm) cc_final: 0.8775 (mm) REVERT: A 596 SER cc_start: 0.9279 (m) cc_final: 0.8692 (p) REVERT: A 633 TRP cc_start: 0.8629 (p-90) cc_final: 0.8300 (p-90) REVERT: A 725 GLU cc_start: 0.8401 (tt0) cc_final: 0.8119 (tt0) REVERT: A 773 GLU cc_start: 0.8379 (tt0) cc_final: 0.8158 (tt0) REVERT: A 790 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8703 (mtmm) REVERT: A 825 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8703 (tptt) REVERT: A 904 TYR cc_start: 0.8525 (m-10) cc_final: 0.8200 (m-10) REVERT: A 986 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8351 (ttmm) REVERT: A 990 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 1017 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 1092 GLU cc_start: 0.7840 (pm20) cc_final: 0.7636 (pm20) REVERT: C 135 PHE cc_start: 0.7492 (m-10) cc_final: 0.7255 (m-80) REVERT: C 177 MET cc_start: 0.5278 (mpp) cc_final: 0.4868 (mmt) REVERT: C 239 GLN cc_start: 0.8145 (tp40) cc_final: 0.7888 (tp40) REVERT: C 275 PHE cc_start: 0.8774 (m-80) cc_final: 0.8434 (m-80) REVERT: C 276 LEU cc_start: 0.9009 (tp) cc_final: 0.8790 (tt) REVERT: C 277 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8873 (mp) REVERT: C 324 GLU cc_start: 0.8012 (pm20) cc_final: 0.7679 (pm20) REVERT: C 342 PHE cc_start: 0.8368 (m-80) cc_final: 0.8077 (m-80) REVERT: C 349 SER cc_start: 0.8303 (m) cc_final: 0.8017 (p) REVERT: C 383 SER cc_start: 0.9042 (t) cc_final: 0.8706 (p) REVERT: C 406 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 434 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8579 (mm) REVERT: C 436 TRP cc_start: 0.6933 (p90) cc_final: 0.6632 (p90) REVERT: C 452 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7406 (ptm160) REVERT: C 495 TYR cc_start: 0.6398 (m-80) cc_final: 0.5969 (m-80) REVERT: C 523 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8037 (p) REVERT: C 565 PHE cc_start: 0.7150 (m-10) cc_final: 0.6667 (m-10) REVERT: C 596 SER cc_start: 0.9222 (m) cc_final: 0.8620 (p) REVERT: C 610 VAL cc_start: 0.8942 (t) cc_final: 0.8617 (m) REVERT: C 737 ASP cc_start: 0.8079 (t0) cc_final: 0.7810 (t0) REVERT: C 790 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8697 (mtmm) REVERT: C 820 ASP cc_start: 0.8356 (t0) cc_final: 0.7979 (m-30) REVERT: C 825 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8543 (tptp) REVERT: C 1037 SER cc_start: 0.9198 (t) cc_final: 0.8881 (p) outliers start: 77 outliers final: 42 residues processed: 636 average time/residue: 0.1733 time to fit residues: 176.1103 Evaluate side-chains 596 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 546 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 388 ASN B 755 GLN B 777 ASN B 957 GLN B1002 GLN B1119 ASN A 317 ASN A 751 ASN C 360 ASN C 969 ASN C1113 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.112250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089868 restraints weight = 59153.979| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.31 r_work: 0.3247 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28173 Z= 0.187 Angle : 0.788 18.319 38538 Z= 0.369 Chirality : 0.049 0.695 4650 Planarity : 0.004 0.050 4761 Dihedral : 13.243 104.510 5953 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.23 % Rotamer: Outliers : 2.88 % Allowed : 13.82 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.58 (0.14), residues: 3273 helix: 1.32 (0.20), residues: 750 sheet: 0.01 (0.18), residues: 723 loop : -1.34 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.021 0.002 TYR C1067 PHE 0.024 0.002 PHE A 168 TRP 0.016 0.002 TRP C 353 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00425 (28014) covalent geometry : angle 0.74002 (38103) SS BOND : bond 0.00523 ( 42) SS BOND : angle 2.36205 ( 84) hydrogen bonds : bond 0.04375 ( 1084) hydrogen bonds : angle 5.97764 ( 2967) link_ALPHA1-4 : bond 0.01511 ( 27) link_ALPHA1-4 : angle 2.80218 ( 81) link_BETA1-4 : bond 0.00498 ( 33) link_BETA1-4 : angle 1.48509 ( 99) link_BETA1-6 : bond 0.01384 ( 3) link_BETA1-6 : angle 2.29194 ( 9) link_NAG-ASN : bond 0.00506 ( 54) link_NAG-ASN : angle 3.21664 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 587 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7962 (m) cc_final: 0.7714 (m) REVERT: B 99 ASN cc_start: 0.8347 (t0) cc_final: 0.8024 (t0) REVERT: B 104 TRP cc_start: 0.7936 (m-90) cc_final: 0.7730 (m-90) REVERT: B 140 PHE cc_start: 0.7856 (p90) cc_final: 0.7478 (p90) REVERT: B 169 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: B 177 MET cc_start: 0.4739 (mpp) cc_final: 0.4411 (mmt) REVERT: B 298 GLU cc_start: 0.8229 (tt0) cc_final: 0.7772 (tt0) REVERT: B 306 PHE cc_start: 0.8864 (m-80) cc_final: 0.8477 (m-80) REVERT: B 315 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8172 (m) REVERT: B 360 ASN cc_start: 0.8545 (t0) cc_final: 0.8285 (t0) REVERT: B 383 SER cc_start: 0.8764 (t) cc_final: 0.7760 (m) REVERT: B 434 ILE cc_start: 0.8933 (mm) cc_final: 0.8657 (mm) REVERT: B 436 TRP cc_start: 0.7100 (p90) cc_final: 0.6732 (p90) REVERT: B 452 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7679 (ptm160) REVERT: B 460 ASN cc_start: 0.8023 (m-40) cc_final: 0.7550 (m110) REVERT: B 523 THR cc_start: 0.8671 (m) cc_final: 0.8225 (p) REVERT: B 537 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8444 (ttpt) REVERT: B 557 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8511 (ptpt) REVERT: B 565 PHE cc_start: 0.7261 (m-10) cc_final: 0.6734 (m-10) REVERT: B 587 ILE cc_start: 0.8933 (mt) cc_final: 0.8647 (tp) REVERT: B 596 SER cc_start: 0.9236 (m) cc_final: 0.8763 (p) REVERT: B 633 TRP cc_start: 0.8546 (p-90) cc_final: 0.7961 (p-90) REVERT: B 642 VAL cc_start: 0.9300 (t) cc_final: 0.9027 (p) REVERT: B 646 ARG cc_start: 0.8728 (tpt170) cc_final: 0.8319 (tpt170) REVERT: B 737 ASP cc_start: 0.7998 (t70) cc_final: 0.7551 (p0) REVERT: B 776 LYS cc_start: 0.8711 (tptm) cc_final: 0.8335 (ttpt) REVERT: B 790 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8464 (mtmm) REVERT: B 808 ASP cc_start: 0.7654 (t0) cc_final: 0.7437 (t0) REVERT: B 1086 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8746 (mtmm) REVERT: B 1107 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8257 (mtt90) REVERT: B 1141 LEU cc_start: 0.8795 (tt) cc_final: 0.8505 (mm) REVERT: B 1146 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7931 (t70) REVERT: A 96 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5218 (tt0) REVERT: A 99 ASN cc_start: 0.8444 (t0) cc_final: 0.7931 (t0) REVERT: A 269 TYR cc_start: 0.7525 (m-80) cc_final: 0.7237 (m-80) REVERT: A 289 VAL cc_start: 0.8978 (t) cc_final: 0.8591 (m) REVERT: A 342 PHE cc_start: 0.8608 (m-80) cc_final: 0.8243 (m-80) REVERT: A 360 ASN cc_start: 0.8618 (t0) cc_final: 0.8192 (t0) REVERT: A 406 GLU cc_start: 0.7869 (mp0) cc_final: 0.7463 (mp0) REVERT: A 452 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8114 (ptm-80) REVERT: A 495 TYR cc_start: 0.5841 (m-80) cc_final: 0.5570 (m-80) REVERT: A 523 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8116 (p) REVERT: A 565 PHE cc_start: 0.7389 (m-10) cc_final: 0.6824 (m-10) REVERT: A 583 GLU cc_start: 0.8008 (pp20) cc_final: 0.7742 (pp20) REVERT: A 584 ILE cc_start: 0.9030 (mm) cc_final: 0.8791 (mm) REVERT: A 596 SER cc_start: 0.9306 (m) cc_final: 0.8729 (p) REVERT: A 633 TRP cc_start: 0.8613 (p-90) cc_final: 0.8299 (p-90) REVERT: A 725 GLU cc_start: 0.8443 (tt0) cc_final: 0.8156 (tt0) REVERT: A 773 GLU cc_start: 0.8390 (tt0) cc_final: 0.8187 (tt0) REVERT: A 790 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8803 (mtmm) REVERT: A 825 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8759 (tptt) REVERT: A 904 TYR cc_start: 0.8529 (m-10) cc_final: 0.8281 (m-10) REVERT: A 986 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8192 (ttmm) REVERT: A 990 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 1107 ARG cc_start: 0.8614 (mtt90) cc_final: 0.8281 (mtt90) REVERT: C 177 MET cc_start: 0.5402 (mpp) cc_final: 0.5110 (mmt) REVERT: C 271 GLN cc_start: 0.8657 (mt0) cc_final: 0.8429 (mt0) REVERT: C 275 PHE cc_start: 0.8775 (m-80) cc_final: 0.8429 (m-80) REVERT: C 276 LEU cc_start: 0.9001 (tp) cc_final: 0.8781 (tt) REVERT: C 324 GLU cc_start: 0.8126 (pm20) cc_final: 0.7733 (pm20) REVERT: C 342 PHE cc_start: 0.8364 (m-80) cc_final: 0.8018 (m-80) REVERT: C 349 SER cc_start: 0.8240 (m) cc_final: 0.7990 (p) REVERT: C 383 SER cc_start: 0.9017 (t) cc_final: 0.8681 (p) REVERT: C 396 TYR cc_start: 0.8133 (m-10) cc_final: 0.7599 (m-10) REVERT: C 436 TRP cc_start: 0.7096 (p90) cc_final: 0.6760 (p90) REVERT: C 452 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7428 (ptm160) REVERT: C 456 PHE cc_start: 0.8035 (m-80) cc_final: 0.7434 (m-80) REVERT: C 495 TYR cc_start: 0.6387 (m-80) cc_final: 0.5929 (m-80) REVERT: C 523 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8214 (p) REVERT: C 562 PHE cc_start: 0.7694 (p90) cc_final: 0.7447 (p90) REVERT: C 565 PHE cc_start: 0.7042 (m-10) cc_final: 0.6503 (m-10) REVERT: C 580 GLN cc_start: 0.8135 (mt0) cc_final: 0.7794 (mm-40) REVERT: C 646 ARG cc_start: 0.8633 (tpt-90) cc_final: 0.8133 (tpt170) REVERT: C 737 ASP cc_start: 0.7961 (t0) cc_final: 0.7683 (t0) REVERT: C 790 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8682 (mtmm) REVERT: C 820 ASP cc_start: 0.8406 (t0) cc_final: 0.8004 (m-30) REVERT: C 868 GLU cc_start: 0.8096 (mp0) cc_final: 0.7871 (mm-30) REVERT: C 1037 SER cc_start: 0.9204 (t) cc_final: 0.8855 (p) REVERT: C 1125 ASN cc_start: 0.8784 (p0) cc_final: 0.8581 (p0) outliers start: 83 outliers final: 50 residues processed: 628 average time/residue: 0.1744 time to fit residues: 172.5397 Evaluate side-chains 613 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 554 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 5 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 957 GLN B1002 GLN B1119 ASN A 751 ASN A 907 ASN A 969 ASN C 360 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090381 restraints weight = 59169.158| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.32 r_work: 0.3254 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28173 Z= 0.168 Angle : 0.769 18.074 38538 Z= 0.357 Chirality : 0.048 0.678 4650 Planarity : 0.004 0.054 4761 Dihedral : 12.653 102.844 5951 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.98 % Favored : 94.84 % Rotamer: Outliers : 3.23 % Allowed : 15.42 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.49 (0.14), residues: 3273 helix: 1.48 (0.20), residues: 744 sheet: 0.03 (0.18), residues: 720 loop : -1.29 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 995 TYR 0.020 0.001 TYR C1067 PHE 0.031 0.002 PHE A 497 TRP 0.015 0.001 TRP B 353 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00380 (28014) covalent geometry : angle 0.72352 (38103) SS BOND : bond 0.00448 ( 42) SS BOND : angle 2.05029 ( 84) hydrogen bonds : bond 0.04146 ( 1084) hydrogen bonds : angle 5.89627 ( 2967) link_ALPHA1-4 : bond 0.01494 ( 27) link_ALPHA1-4 : angle 3.00560 ( 81) link_BETA1-4 : bond 0.00379 ( 33) link_BETA1-4 : angle 1.33730 ( 99) link_BETA1-6 : bond 0.01409 ( 3) link_BETA1-6 : angle 2.35429 ( 9) link_NAG-ASN : bond 0.00435 ( 54) link_NAG-ASN : angle 3.05936 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 597 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7917 (m) cc_final: 0.7687 (m) REVERT: B 96 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5485 (tt0) REVERT: B 99 ASN cc_start: 0.8432 (t0) cc_final: 0.7930 (t0) REVERT: B 140 PHE cc_start: 0.7827 (p90) cc_final: 0.7415 (p90) REVERT: B 169 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 289 VAL cc_start: 0.8980 (t) cc_final: 0.8661 (m) REVERT: B 306 PHE cc_start: 0.8920 (m-80) cc_final: 0.8525 (m-80) REVERT: B 315 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8368 (p) REVERT: B 360 ASN cc_start: 0.8626 (t0) cc_final: 0.8383 (t0) REVERT: B 434 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8664 (mm) REVERT: B 436 TRP cc_start: 0.7210 (p90) cc_final: 0.6828 (p90) REVERT: B 452 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7650 (ptm160) REVERT: B 460 ASN cc_start: 0.8067 (m-40) cc_final: 0.7667 (m110) REVERT: B 523 THR cc_start: 0.8744 (m) cc_final: 0.8317 (p) REVERT: B 537 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8385 (ttpt) REVERT: B 557 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8481 (ptpt) REVERT: B 565 PHE cc_start: 0.7252 (m-10) cc_final: 0.6668 (m-10) REVERT: B 587 ILE cc_start: 0.8904 (mt) cc_final: 0.8652 (tp) REVERT: B 596 SER cc_start: 0.9246 (m) cc_final: 0.8749 (p) REVERT: B 642 VAL cc_start: 0.9325 (t) cc_final: 0.9062 (p) REVERT: B 650 LEU cc_start: 0.8503 (tp) cc_final: 0.8282 (tp) REVERT: B 737 ASP cc_start: 0.7897 (t70) cc_final: 0.7409 (p0) REVERT: B 762 GLN cc_start: 0.8689 (tt0) cc_final: 0.8428 (mt0) REVERT: B 776 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8280 (ttpt) REVERT: B 808 ASP cc_start: 0.7662 (t0) cc_final: 0.7347 (t0) REVERT: B 815 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8588 (ttm110) REVERT: B 820 ASP cc_start: 0.8076 (t0) cc_final: 0.7683 (m-30) REVERT: B 1050 MET cc_start: 0.8728 (ptm) cc_final: 0.8341 (ptm) REVERT: B 1107 ARG cc_start: 0.8664 (mtt90) cc_final: 0.8224 (mtt90) REVERT: A 99 ASN cc_start: 0.8524 (t0) cc_final: 0.8242 (t0) REVERT: A 169 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: A 269 TYR cc_start: 0.7553 (m-80) cc_final: 0.7221 (m-80) REVERT: A 289 VAL cc_start: 0.8923 (t) cc_final: 0.8533 (m) REVERT: A 360 ASN cc_start: 0.8669 (t0) cc_final: 0.8226 (t0) REVERT: A 406 GLU cc_start: 0.7941 (mp0) cc_final: 0.7534 (mp0) REVERT: A 408 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8321 (ttp80) REVERT: A 456 PHE cc_start: 0.8218 (m-80) cc_final: 0.8006 (m-80) REVERT: A 495 TYR cc_start: 0.6215 (m-80) cc_final: 0.5981 (m-80) REVERT: A 523 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8157 (p) REVERT: A 565 PHE cc_start: 0.7342 (m-10) cc_final: 0.6751 (m-10) REVERT: A 596 SER cc_start: 0.9318 (m) cc_final: 0.8731 (p) REVERT: A 633 TRP cc_start: 0.8665 (p-90) cc_final: 0.8307 (p-90) REVERT: A 725 GLU cc_start: 0.8431 (tt0) cc_final: 0.8135 (tt0) REVERT: A 773 GLU cc_start: 0.8365 (tt0) cc_final: 0.8155 (tt0) REVERT: A 790 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8804 (mtmm) REVERT: A 825 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8722 (tptt) REVERT: A 904 TYR cc_start: 0.8536 (m-10) cc_final: 0.8274 (m-10) REVERT: A 964 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8950 (mtmm) REVERT: A 986 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8127 (ttmm) REVERT: A 990 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7817 (mt-10) REVERT: C 177 MET cc_start: 0.5449 (mpp) cc_final: 0.5230 (mpp) REVERT: C 275 PHE cc_start: 0.8782 (m-80) cc_final: 0.8423 (m-80) REVERT: C 276 LEU cc_start: 0.8992 (tp) cc_final: 0.8760 (tt) REVERT: C 298 GLU cc_start: 0.8382 (tp30) cc_final: 0.8123 (tp30) REVERT: C 324 GLU cc_start: 0.8146 (pm20) cc_final: 0.7806 (pm20) REVERT: C 349 SER cc_start: 0.8225 (m) cc_final: 0.7895 (p) REVERT: C 383 SER cc_start: 0.9033 (t) cc_final: 0.8679 (p) REVERT: C 406 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7882 (mm-30) REVERT: C 434 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8617 (mm) REVERT: C 436 TRP cc_start: 0.7178 (p90) cc_final: 0.6700 (p90) REVERT: C 452 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7703 (ptm160) REVERT: C 486 PHE cc_start: 0.7297 (t80) cc_final: 0.6957 (t80) REVERT: C 523 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 565 PHE cc_start: 0.6998 (m-10) cc_final: 0.6431 (m-10) REVERT: C 587 ILE cc_start: 0.8825 (mt) cc_final: 0.8550 (tp) REVERT: C 596 SER cc_start: 0.9187 (m) cc_final: 0.8608 (p) REVERT: C 633 TRP cc_start: 0.8480 (p-90) cc_final: 0.7087 (p-90) REVERT: C 661 GLU cc_start: 0.7853 (tp30) cc_final: 0.7548 (tp30) REVERT: C 737 ASP cc_start: 0.7997 (t0) cc_final: 0.7767 (t0) REVERT: C 776 LYS cc_start: 0.8723 (tptm) cc_final: 0.8393 (ttpt) REVERT: C 790 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8639 (mtmm) REVERT: C 820 ASP cc_start: 0.8411 (t0) cc_final: 0.7987 (m-30) REVERT: C 994 ASP cc_start: 0.8295 (t70) cc_final: 0.8024 (t0) REVERT: C 1037 SER cc_start: 0.9214 (t) cc_final: 0.8865 (p) outliers start: 93 outliers final: 56 residues processed: 643 average time/residue: 0.1768 time to fit residues: 179.1362 Evaluate side-chains 640 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 571 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 957 GLN B1002 GLN B1119 ASN A 751 ASN A 969 ASN A1119 ASN C 360 ASN C 580 GLN C 872 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.112404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090058 restraints weight = 59579.690| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.32 r_work: 0.3251 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28173 Z= 0.177 Angle : 0.764 15.089 38538 Z= 0.355 Chirality : 0.047 0.673 4650 Planarity : 0.004 0.054 4761 Dihedral : 12.078 101.903 5951 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.80 % Favored : 95.02 % Rotamer: Outliers : 3.40 % Allowed : 16.22 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.47 (0.14), residues: 3273 helix: 1.51 (0.20), residues: 744 sheet: -0.06 (0.18), residues: 744 loop : -1.25 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 995 TYR 0.024 0.002 TYR A 495 PHE 0.032 0.002 PHE A 497 TRP 0.014 0.001 TRP B 353 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00399 (28014) covalent geometry : angle 0.72606 (38103) SS BOND : bond 0.00484 ( 42) SS BOND : angle 2.13646 ( 84) hydrogen bonds : bond 0.04064 ( 1084) hydrogen bonds : angle 5.87637 ( 2967) link_ALPHA1-4 : bond 0.01570 ( 27) link_ALPHA1-4 : angle 2.99121 ( 81) link_BETA1-4 : bond 0.00391 ( 33) link_BETA1-4 : angle 1.34818 ( 99) link_BETA1-6 : bond 0.01459 ( 3) link_BETA1-6 : angle 2.49325 ( 9) link_NAG-ASN : bond 0.00324 ( 54) link_NAG-ASN : angle 2.59196 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 596 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7931 (m) cc_final: 0.7700 (m) REVERT: B 52 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 96 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5400 (tt0) REVERT: B 99 ASN cc_start: 0.8425 (t0) cc_final: 0.7974 (t0) REVERT: B 140 PHE cc_start: 0.7825 (p90) cc_final: 0.7431 (p90) REVERT: B 169 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: B 289 VAL cc_start: 0.8963 (t) cc_final: 0.8650 (m) REVERT: B 298 GLU cc_start: 0.8265 (tt0) cc_final: 0.8048 (tp30) REVERT: B 306 PHE cc_start: 0.8948 (m-80) cc_final: 0.8605 (m-80) REVERT: B 360 ASN cc_start: 0.8638 (t0) cc_final: 0.8421 (t0) REVERT: B 383 SER cc_start: 0.8713 (t) cc_final: 0.8058 (m) REVERT: B 434 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 436 TRP cc_start: 0.7164 (p90) cc_final: 0.6719 (p90) REVERT: B 452 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7685 (ptm160) REVERT: B 456 PHE cc_start: 0.7952 (m-80) cc_final: 0.7555 (m-80) REVERT: B 460 ASN cc_start: 0.7961 (m-40) cc_final: 0.7567 (m110) REVERT: B 523 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 537 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8438 (ttpt) REVERT: B 557 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8502 (ptpt) REVERT: B 565 PHE cc_start: 0.7233 (m-10) cc_final: 0.6651 (m-10) REVERT: B 587 ILE cc_start: 0.8910 (mt) cc_final: 0.8688 (tp) REVERT: B 596 SER cc_start: 0.9254 (m) cc_final: 0.8751 (p) REVERT: B 642 VAL cc_start: 0.9342 (t) cc_final: 0.9084 (p) REVERT: B 650 LEU cc_start: 0.8480 (tp) cc_final: 0.8247 (tp) REVERT: B 762 GLN cc_start: 0.8694 (tt0) cc_final: 0.8468 (mt0) REVERT: B 776 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8275 (ttpt) REVERT: B 808 ASP cc_start: 0.7666 (t0) cc_final: 0.7354 (t0) REVERT: B 820 ASP cc_start: 0.8152 (t0) cc_final: 0.7861 (m-30) REVERT: B 1107 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8202 (mtt90) REVERT: A 99 ASN cc_start: 0.8505 (t0) cc_final: 0.8226 (t0) REVERT: A 169 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: A 269 TYR cc_start: 0.7542 (m-80) cc_final: 0.7210 (m-80) REVERT: A 289 VAL cc_start: 0.8900 (t) cc_final: 0.8511 (m) REVERT: A 360 ASN cc_start: 0.8690 (t0) cc_final: 0.8264 (t0) REVERT: A 406 GLU cc_start: 0.7932 (mp0) cc_final: 0.7528 (mp0) REVERT: A 408 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: A 523 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 565 PHE cc_start: 0.7355 (m-10) cc_final: 0.6764 (m-10) REVERT: A 596 SER cc_start: 0.9317 (m) cc_final: 0.8753 (p) REVERT: A 633 TRP cc_start: 0.8664 (p-90) cc_final: 0.8279 (p-90) REVERT: A 725 GLU cc_start: 0.8436 (tt0) cc_final: 0.8135 (tt0) REVERT: A 773 GLU cc_start: 0.8369 (tt0) cc_final: 0.8164 (tt0) REVERT: A 790 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8792 (mtmm) REVERT: A 825 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8767 (tptt) REVERT: A 904 TYR cc_start: 0.8519 (m-10) cc_final: 0.8261 (m-10) REVERT: A 964 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8944 (mtmm) REVERT: A 986 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8089 (ttmm) REVERT: A 990 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 177 MET cc_start: 0.5439 (mpp) cc_final: 0.5085 (mmt) REVERT: C 271 GLN cc_start: 0.8708 (mt0) cc_final: 0.8400 (mt0) REVERT: C 273 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7712 (mtt-85) REVERT: C 275 PHE cc_start: 0.8772 (m-80) cc_final: 0.8382 (m-80) REVERT: C 276 LEU cc_start: 0.9014 (tp) cc_final: 0.8760 (tt) REVERT: C 278 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8508 (ttmt) REVERT: C 298 GLU cc_start: 0.8431 (tp30) cc_final: 0.8212 (tp30) REVERT: C 324 GLU cc_start: 0.8129 (pm20) cc_final: 0.7689 (pm20) REVERT: C 349 SER cc_start: 0.8198 (m) cc_final: 0.7864 (p) REVERT: C 383 SER cc_start: 0.9036 (t) cc_final: 0.8668 (p) REVERT: C 406 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 434 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8596 (mm) REVERT: C 436 TRP cc_start: 0.7244 (p90) cc_final: 0.6790 (p90) REVERT: C 452 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7660 (ptm160) REVERT: C 523 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8407 (p) REVERT: C 565 PHE cc_start: 0.6985 (m-10) cc_final: 0.6418 (m-10) REVERT: C 587 ILE cc_start: 0.8856 (mt) cc_final: 0.8583 (tp) REVERT: C 596 SER cc_start: 0.9192 (m) cc_final: 0.8646 (p) REVERT: C 633 TRP cc_start: 0.8460 (p-90) cc_final: 0.6958 (p-90) REVERT: C 646 ARG cc_start: 0.8721 (tpt-90) cc_final: 0.8174 (tpt170) REVERT: C 661 GLU cc_start: 0.8248 (tp30) cc_final: 0.8013 (tp30) REVERT: C 675 GLN cc_start: 0.7506 (pp30) cc_final: 0.7129 (tm-30) REVERT: C 737 ASP cc_start: 0.8039 (t0) cc_final: 0.7819 (t0) REVERT: C 776 LYS cc_start: 0.8714 (tptm) cc_final: 0.8383 (ttpt) REVERT: C 790 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8615 (mtmm) REVERT: C 820 ASP cc_start: 0.8398 (t0) cc_final: 0.7994 (m-30) REVERT: C 994 ASP cc_start: 0.8285 (t70) cc_final: 0.8024 (t0) REVERT: C 1037 SER cc_start: 0.9217 (t) cc_final: 0.8869 (p) outliers start: 98 outliers final: 63 residues processed: 642 average time/residue: 0.1767 time to fit residues: 180.0388 Evaluate side-chains 644 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 569 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 200 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 218 optimal weight: 0.7980 chunk 140 optimal weight: 0.2980 chunk 247 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 GLN B 777 ASN B 957 GLN B1119 ASN A 969 ASN C 360 ASN C 969 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089587 restraints weight = 59005.375| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.31 r_work: 0.3244 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28173 Z= 0.186 Angle : 0.774 15.212 38538 Z= 0.358 Chirality : 0.047 0.676 4650 Planarity : 0.004 0.057 4761 Dihedral : 11.383 101.361 5949 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 3.19 % Allowed : 17.29 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.46 (0.14), residues: 3273 helix: 1.60 (0.20), residues: 738 sheet: -0.17 (0.18), residues: 705 loop : -1.20 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 995 TYR 0.023 0.002 TYR A 495 PHE 0.029 0.002 PHE A 456 TRP 0.018 0.001 TRP C 353 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00422 (28014) covalent geometry : angle 0.73642 (38103) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.98077 ( 84) hydrogen bonds : bond 0.04079 ( 1084) hydrogen bonds : angle 5.85340 ( 2967) link_ALPHA1-4 : bond 0.01641 ( 27) link_ALPHA1-4 : angle 3.21786 ( 81) link_BETA1-4 : bond 0.00363 ( 33) link_BETA1-4 : angle 1.29513 ( 99) link_BETA1-6 : bond 0.01444 ( 3) link_BETA1-6 : angle 2.53176 ( 9) link_NAG-ASN : bond 0.00310 ( 54) link_NAG-ASN : angle 2.51903 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 598 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7998 (m) cc_final: 0.7772 (m) REVERT: B 52 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 96 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5297 (tt0) REVERT: B 99 ASN cc_start: 0.8389 (t0) cc_final: 0.8026 (t0) REVERT: B 140 PHE cc_start: 0.7853 (p90) cc_final: 0.7455 (p90) REVERT: B 153 MET cc_start: 0.6246 (tmm) cc_final: 0.6015 (tpt) REVERT: B 169 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: B 289 VAL cc_start: 0.8994 (t) cc_final: 0.8749 (m) REVERT: B 314 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 319 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.8216 (ttm110) REVERT: B 360 ASN cc_start: 0.8648 (t0) cc_final: 0.8433 (t0) REVERT: B 383 SER cc_start: 0.8706 (t) cc_final: 0.8078 (m) REVERT: B 436 TRP cc_start: 0.7163 (p90) cc_final: 0.6752 (p90) REVERT: B 452 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7684 (ptm160) REVERT: B 460 ASN cc_start: 0.7876 (m-40) cc_final: 0.7521 (m110) REVERT: B 523 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 532 ASN cc_start: 0.8471 (t0) cc_final: 0.8231 (t0) REVERT: B 537 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8370 (ttpt) REVERT: B 557 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8524 (ptpt) REVERT: B 565 PHE cc_start: 0.7224 (m-10) cc_final: 0.6656 (m-10) REVERT: B 596 SER cc_start: 0.9250 (m) cc_final: 0.8788 (p) REVERT: B 642 VAL cc_start: 0.9352 (t) cc_final: 0.9026 (p) REVERT: B 650 LEU cc_start: 0.8514 (tp) cc_final: 0.8283 (tp) REVERT: B 762 GLN cc_start: 0.8664 (tt0) cc_final: 0.8441 (mt0) REVERT: B 776 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8358 (ttpt) REVERT: B 815 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8378 (tpp80) REVERT: B 820 ASP cc_start: 0.8208 (t0) cc_final: 0.7944 (m-30) REVERT: B 1017 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 1107 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8241 (mtt90) REVERT: A 99 ASN cc_start: 0.8437 (t0) cc_final: 0.8163 (t0) REVERT: A 153 MET cc_start: 0.6024 (tpt) cc_final: 0.5648 (ppp) REVERT: A 169 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: A 269 TYR cc_start: 0.7542 (m-80) cc_final: 0.7235 (m-80) REVERT: A 289 VAL cc_start: 0.8933 (t) cc_final: 0.8569 (m) REVERT: A 360 ASN cc_start: 0.8677 (t0) cc_final: 0.8260 (t0) REVERT: A 406 GLU cc_start: 0.7878 (mp0) cc_final: 0.7489 (mp0) REVERT: A 523 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 557 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8497 (ptpt) REVERT: A 565 PHE cc_start: 0.7402 (m-10) cc_final: 0.6808 (m-10) REVERT: A 596 SER cc_start: 0.9305 (m) cc_final: 0.8789 (p) REVERT: A 633 TRP cc_start: 0.8677 (p-90) cc_final: 0.8273 (p-90) REVERT: A 725 GLU cc_start: 0.8422 (tt0) cc_final: 0.8144 (tt0) REVERT: A 773 GLU cc_start: 0.8366 (tt0) cc_final: 0.8145 (tt0) REVERT: A 790 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8780 (mtmm) REVERT: A 825 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8790 (tptt) REVERT: A 904 TYR cc_start: 0.8532 (m-10) cc_final: 0.8325 (m-10) REVERT: A 964 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8986 (mtmm) REVERT: A 986 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8127 (ttmm) REVERT: A 990 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 177 MET cc_start: 0.5418 (mpp) cc_final: 0.5115 (mmt) REVERT: C 188 ASN cc_start: 0.7679 (m-40) cc_final: 0.7111 (t0) REVERT: C 271 GLN cc_start: 0.8709 (mt0) cc_final: 0.8388 (mt0) REVERT: C 273 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7739 (mtt-85) REVERT: C 275 PHE cc_start: 0.8771 (m-80) cc_final: 0.8402 (m-80) REVERT: C 276 LEU cc_start: 0.9013 (tp) cc_final: 0.8710 (tt) REVERT: C 298 GLU cc_start: 0.8451 (tp30) cc_final: 0.8220 (tp30) REVERT: C 324 GLU cc_start: 0.8191 (pm20) cc_final: 0.7748 (pm20) REVERT: C 349 SER cc_start: 0.8090 (m) cc_final: 0.7800 (p) REVERT: C 383 SER cc_start: 0.8947 (t) cc_final: 0.8574 (p) REVERT: C 406 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 434 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8583 (mm) REVERT: C 436 TRP cc_start: 0.7194 (p90) cc_final: 0.6792 (p90) REVERT: C 452 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7591 (ptm160) REVERT: C 523 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 565 PHE cc_start: 0.7016 (m-10) cc_final: 0.6451 (m-10) REVERT: C 587 ILE cc_start: 0.8874 (mt) cc_final: 0.8642 (tp) REVERT: C 633 TRP cc_start: 0.8460 (p-90) cc_final: 0.6961 (p-90) REVERT: C 674 TYR cc_start: 0.8820 (t80) cc_final: 0.8533 (t80) REVERT: C 737 ASP cc_start: 0.8021 (t0) cc_final: 0.7818 (t0) REVERT: C 776 LYS cc_start: 0.8758 (tptm) cc_final: 0.8455 (ttpt) REVERT: C 790 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8584 (mtmm) REVERT: C 820 ASP cc_start: 0.8408 (t0) cc_final: 0.8022 (m-30) REVERT: C 994 ASP cc_start: 0.8254 (t70) cc_final: 0.7997 (t0) REVERT: C 1037 SER cc_start: 0.9204 (t) cc_final: 0.8859 (p) outliers start: 92 outliers final: 62 residues processed: 636 average time/residue: 0.1691 time to fit residues: 170.8710 Evaluate side-chains 633 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 559 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 35 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 154 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 258 optimal weight: 0.0070 chunk 86 optimal weight: 0.5980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 777 ASN B 957 GLN B1119 ASN A 969 ASN A1005 GLN C 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090264 restraints weight = 59478.498| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.32 r_work: 0.3253 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28173 Z= 0.165 Angle : 0.770 15.081 38538 Z= 0.356 Chirality : 0.046 0.671 4650 Planarity : 0.004 0.057 4761 Dihedral : 10.300 98.884 5948 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.68 % Rotamer: Outliers : 3.12 % Allowed : 17.57 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.40 (0.14), residues: 3273 helix: 1.63 (0.20), residues: 738 sheet: -0.13 (0.18), residues: 729 loop : -1.16 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1107 TYR 0.027 0.001 TYR A 453 PHE 0.033 0.002 PHE A 497 TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00370 (28014) covalent geometry : angle 0.73459 (38103) SS BOND : bond 0.00485 ( 42) SS BOND : angle 1.72999 ( 84) hydrogen bonds : bond 0.03914 ( 1084) hydrogen bonds : angle 5.82667 ( 2967) link_ALPHA1-4 : bond 0.01735 ( 27) link_ALPHA1-4 : angle 3.26211 ( 81) link_BETA1-4 : bond 0.00378 ( 33) link_BETA1-4 : angle 1.24711 ( 99) link_BETA1-6 : bond 0.01768 ( 3) link_BETA1-6 : angle 2.46400 ( 9) link_NAG-ASN : bond 0.00303 ( 54) link_NAG-ASN : angle 2.46078 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 588 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7966 (m) cc_final: 0.7731 (m) REVERT: B 52 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 96 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5455 (tt0) REVERT: B 99 ASN cc_start: 0.8427 (t0) cc_final: 0.8058 (t0) REVERT: B 140 PHE cc_start: 0.7862 (p90) cc_final: 0.7460 (p90) REVERT: B 153 MET cc_start: 0.6396 (tmm) cc_final: 0.6022 (tpt) REVERT: B 169 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: B 289 VAL cc_start: 0.8947 (t) cc_final: 0.8691 (m) REVERT: B 319 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8185 (ttm110) REVERT: B 360 ASN cc_start: 0.8637 (t0) cc_final: 0.8222 (t0) REVERT: B 383 SER cc_start: 0.8760 (t) cc_final: 0.8175 (m) REVERT: B 434 ILE cc_start: 0.8883 (mm) cc_final: 0.8624 (mm) REVERT: B 436 TRP cc_start: 0.7202 (p90) cc_final: 0.6797 (p90) REVERT: B 452 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7748 (ptm160) REVERT: B 460 ASN cc_start: 0.7874 (m-40) cc_final: 0.7524 (m110) REVERT: B 523 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8363 (p) REVERT: B 532 ASN cc_start: 0.8460 (t0) cc_final: 0.8193 (t0) REVERT: B 537 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8368 (ttpt) REVERT: B 557 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8558 (ptpt) REVERT: B 565 PHE cc_start: 0.7200 (m-10) cc_final: 0.6591 (m-10) REVERT: B 596 SER cc_start: 0.9262 (m) cc_final: 0.8764 (p) REVERT: B 642 VAL cc_start: 0.9335 (t) cc_final: 0.9073 (p) REVERT: B 650 LEU cc_start: 0.8439 (tp) cc_final: 0.8211 (tp) REVERT: B 762 GLN cc_start: 0.8668 (tt0) cc_final: 0.8442 (mt0) REVERT: B 776 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8259 (ttpt) REVERT: B 815 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8383 (tpp80) REVERT: B 820 ASP cc_start: 0.8170 (t0) cc_final: 0.7852 (m-30) REVERT: B 912 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 918 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8346 (mt-10) REVERT: B 1017 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 1107 ARG cc_start: 0.8699 (mtt90) cc_final: 0.8256 (mtt90) REVERT: A 99 ASN cc_start: 0.8462 (t0) cc_final: 0.8209 (t0) REVERT: A 153 MET cc_start: 0.6041 (tpt) cc_final: 0.5693 (ppp) REVERT: A 169 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7741 (mm-30) REVERT: A 289 VAL cc_start: 0.8890 (t) cc_final: 0.8525 (m) REVERT: A 357 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7747 (tpp-160) REVERT: A 360 ASN cc_start: 0.8663 (t0) cc_final: 0.8243 (t0) REVERT: A 406 GLU cc_start: 0.7954 (mp0) cc_final: 0.7520 (mp0) REVERT: A 456 PHE cc_start: 0.8210 (m-80) cc_final: 0.7852 (m-80) REVERT: A 523 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 557 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8580 (ptpt) REVERT: A 565 PHE cc_start: 0.7389 (m-10) cc_final: 0.6831 (m-10) REVERT: A 583 GLU cc_start: 0.7909 (pp20) cc_final: 0.7677 (pp20) REVERT: A 596 SER cc_start: 0.9299 (m) cc_final: 0.8775 (p) REVERT: A 633 TRP cc_start: 0.8736 (p-90) cc_final: 0.7895 (p-90) REVERT: A 725 GLU cc_start: 0.8399 (tt0) cc_final: 0.8095 (tt0) REVERT: A 773 GLU cc_start: 0.8390 (tt0) cc_final: 0.8166 (tt0) REVERT: A 790 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8762 (mtmm) REVERT: A 825 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8774 (tptt) REVERT: A 904 TYR cc_start: 0.8538 (m-10) cc_final: 0.8288 (m-10) REVERT: A 964 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8966 (mtmm) REVERT: A 986 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8128 (ttmm) REVERT: A 990 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 1107 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8316 (mtt90) REVERT: C 96 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: C 102 ARG cc_start: 0.7465 (mmt90) cc_final: 0.7215 (mmt-90) REVERT: C 169 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: C 177 MET cc_start: 0.5580 (mpp) cc_final: 0.5249 (mpp) REVERT: C 188 ASN cc_start: 0.7714 (m-40) cc_final: 0.7140 (t0) REVERT: C 271 GLN cc_start: 0.8737 (mt0) cc_final: 0.8393 (mt0) REVERT: C 273 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7716 (mtt-85) REVERT: C 276 LEU cc_start: 0.9010 (tp) cc_final: 0.8747 (tt) REVERT: C 324 GLU cc_start: 0.8209 (pm20) cc_final: 0.7762 (pm20) REVERT: C 342 PHE cc_start: 0.8590 (m-80) cc_final: 0.8241 (m-80) REVERT: C 349 SER cc_start: 0.8110 (m) cc_final: 0.7812 (p) REVERT: C 370 ASN cc_start: 0.7572 (p0) cc_final: 0.7222 (m-40) REVERT: C 383 SER cc_start: 0.8868 (t) cc_final: 0.8406 (p) REVERT: C 406 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7824 (mm-30) REVERT: C 434 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8652 (pt) REVERT: C 436 TRP cc_start: 0.7282 (p90) cc_final: 0.6858 (p90) REVERT: C 452 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7613 (ptm160) REVERT: C 456 PHE cc_start: 0.7792 (m-80) cc_final: 0.7459 (m-80) REVERT: C 523 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 565 PHE cc_start: 0.6964 (m-10) cc_final: 0.6382 (m-10) REVERT: C 587 ILE cc_start: 0.8837 (mt) cc_final: 0.8602 (tp) REVERT: C 633 TRP cc_start: 0.8483 (p-90) cc_final: 0.6942 (p-90) REVERT: C 737 ASP cc_start: 0.8038 (t0) cc_final: 0.7811 (t0) REVERT: C 790 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8560 (mtmm) REVERT: C 994 ASP cc_start: 0.8248 (t70) cc_final: 0.7980 (t0) REVERT: C 1037 SER cc_start: 0.9219 (t) cc_final: 0.8897 (p) outliers start: 90 outliers final: 57 residues processed: 635 average time/residue: 0.1715 time to fit residues: 173.0699 Evaluate side-chains 639 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 567 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 188 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN B 957 GLN B1119 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN C 360 ASN C 935 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090655 restraints weight = 59419.261| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.31 r_work: 0.3263 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28173 Z= 0.161 Angle : 0.768 14.881 38538 Z= 0.356 Chirality : 0.046 0.654 4650 Planarity : 0.004 0.060 4761 Dihedral : 9.217 96.405 5948 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.47 % Favored : 94.35 % Rotamer: Outliers : 2.74 % Allowed : 18.40 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.35 (0.14), residues: 3273 helix: 1.59 (0.20), residues: 741 sheet: 0.01 (0.19), residues: 705 loop : -1.14 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.026 0.001 TYR A 495 PHE 0.025 0.001 PHE C 140 TRP 0.015 0.001 TRP C 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (28014) covalent geometry : angle 0.73143 (38103) SS BOND : bond 0.00548 ( 42) SS BOND : angle 1.96966 ( 84) hydrogen bonds : bond 0.03870 ( 1084) hydrogen bonds : angle 5.79777 ( 2967) link_ALPHA1-4 : bond 0.01818 ( 27) link_ALPHA1-4 : angle 3.34189 ( 81) link_BETA1-4 : bond 0.00367 ( 33) link_BETA1-4 : angle 1.26762 ( 99) link_BETA1-6 : bond 0.01998 ( 3) link_BETA1-6 : angle 2.12969 ( 9) link_NAG-ASN : bond 0.00297 ( 54) link_NAG-ASN : angle 2.40570 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 583 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7951 (m) cc_final: 0.7729 (m) REVERT: B 52 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 96 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5623 (tt0) REVERT: B 99 ASN cc_start: 0.8405 (t0) cc_final: 0.7988 (t0) REVERT: B 140 PHE cc_start: 0.7881 (p90) cc_final: 0.7470 (p90) REVERT: B 153 MET cc_start: 0.6390 (tmm) cc_final: 0.6010 (tpt) REVERT: B 169 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: B 289 VAL cc_start: 0.8890 (t) cc_final: 0.8626 (m) REVERT: B 314 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8453 (mm-40) REVERT: B 360 ASN cc_start: 0.8638 (t0) cc_final: 0.8222 (t0) REVERT: B 383 SER cc_start: 0.8815 (t) cc_final: 0.8178 (m) REVERT: B 434 ILE cc_start: 0.8906 (mm) cc_final: 0.8660 (mm) REVERT: B 436 TRP cc_start: 0.7185 (p90) cc_final: 0.6779 (p90) REVERT: B 452 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7756 (ptm160) REVERT: B 460 ASN cc_start: 0.7861 (m-40) cc_final: 0.7516 (m110) REVERT: B 523 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8394 (p) REVERT: B 537 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8360 (ttpt) REVERT: B 557 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8598 (ptpt) REVERT: B 565 PHE cc_start: 0.7171 (m-10) cc_final: 0.6563 (m-10) REVERT: B 596 SER cc_start: 0.9253 (m) cc_final: 0.8736 (p) REVERT: B 642 VAL cc_start: 0.9339 (t) cc_final: 0.9080 (p) REVERT: B 650 LEU cc_start: 0.8451 (tp) cc_final: 0.8236 (tp) REVERT: B 762 GLN cc_start: 0.8660 (tt0) cc_final: 0.8450 (mt0) REVERT: B 776 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8312 (ttpt) REVERT: B 815 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8465 (tpp80) REVERT: B 820 ASP cc_start: 0.8167 (t0) cc_final: 0.7841 (m-30) REVERT: B 912 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 918 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8348 (mt-10) REVERT: B 1017 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8272 (tp30) REVERT: B 1107 ARG cc_start: 0.8712 (mtt90) cc_final: 0.8276 (mtt90) REVERT: A 29 THR cc_start: 0.7969 (m) cc_final: 0.7758 (m) REVERT: A 99 ASN cc_start: 0.8495 (t0) cc_final: 0.8279 (t0) REVERT: A 153 MET cc_start: 0.6030 (tpt) cc_final: 0.5632 (ppp) REVERT: A 169 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 289 VAL cc_start: 0.8968 (t) cc_final: 0.8541 (m) REVERT: A 297 SER cc_start: 0.8778 (m) cc_final: 0.8409 (m) REVERT: A 349 SER cc_start: 0.8146 (m) cc_final: 0.7880 (p) REVERT: A 360 ASN cc_start: 0.8679 (t0) cc_final: 0.8269 (t0) REVERT: A 406 GLU cc_start: 0.7985 (mp0) cc_final: 0.7549 (mp0) REVERT: A 456 PHE cc_start: 0.8212 (m-80) cc_final: 0.7987 (m-80) REVERT: A 523 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8264 (p) REVERT: A 557 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8654 (ptpt) REVERT: A 565 PHE cc_start: 0.7330 (m-10) cc_final: 0.6805 (m-10) REVERT: A 596 SER cc_start: 0.9290 (m) cc_final: 0.8786 (p) REVERT: A 633 TRP cc_start: 0.8724 (p-90) cc_final: 0.7901 (p-90) REVERT: A 725 GLU cc_start: 0.8411 (tt0) cc_final: 0.8088 (tt0) REVERT: A 762 GLN cc_start: 0.8450 (tt0) cc_final: 0.8191 (mt0) REVERT: A 773 GLU cc_start: 0.8343 (tt0) cc_final: 0.8139 (tt0) REVERT: A 790 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8769 (mtmm) REVERT: A 825 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8776 (tptt) REVERT: A 904 TYR cc_start: 0.8547 (m-10) cc_final: 0.8298 (m-10) REVERT: A 986 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8043 (ttmm) REVERT: A 990 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 102 ARG cc_start: 0.7510 (mmt90) cc_final: 0.7246 (mmt-90) REVERT: C 169 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: C 177 MET cc_start: 0.5556 (mpp) cc_final: 0.5297 (mpp) REVERT: C 188 ASN cc_start: 0.7715 (m-40) cc_final: 0.7160 (t0) REVERT: C 239 GLN cc_start: 0.8316 (tp40) cc_final: 0.8108 (tp40) REVERT: C 271 GLN cc_start: 0.8727 (mt0) cc_final: 0.8369 (mt0) REVERT: C 273 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7220 (mtt-85) REVERT: C 276 LEU cc_start: 0.9018 (tp) cc_final: 0.8786 (tt) REVERT: C 324 GLU cc_start: 0.8241 (pm20) cc_final: 0.7785 (pm20) REVERT: C 342 PHE cc_start: 0.8621 (m-80) cc_final: 0.8275 (m-80) REVERT: C 349 SER cc_start: 0.8073 (m) cc_final: 0.7810 (p) REVERT: C 370 ASN cc_start: 0.7573 (p0) cc_final: 0.7259 (m-40) REVERT: C 383 SER cc_start: 0.8838 (t) cc_final: 0.8362 (p) REVERT: C 402 ILE cc_start: 0.8784 (tp) cc_final: 0.8507 (tp) REVERT: C 406 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7792 (tp30) REVERT: C 434 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8627 (pt) REVERT: C 436 TRP cc_start: 0.7297 (p90) cc_final: 0.6847 (p90) REVERT: C 452 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7503 (ptm160) REVERT: C 456 PHE cc_start: 0.7756 (m-80) cc_final: 0.7411 (m-80) REVERT: C 495 TYR cc_start: 0.6598 (m-80) cc_final: 0.6045 (m-80) REVERT: C 523 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 565 PHE cc_start: 0.6961 (m-10) cc_final: 0.6345 (m-10) REVERT: C 587 ILE cc_start: 0.8813 (mt) cc_final: 0.8570 (tp) REVERT: C 633 TRP cc_start: 0.8494 (p-90) cc_final: 0.6934 (p-90) REVERT: C 663 ASP cc_start: 0.8007 (t0) cc_final: 0.7768 (t0) REVERT: C 675 GLN cc_start: 0.7577 (pp30) cc_final: 0.7242 (tm-30) REVERT: C 737 ASP cc_start: 0.8036 (t0) cc_final: 0.7801 (t0) REVERT: C 776 LYS cc_start: 0.8681 (tptm) cc_final: 0.8343 (tmmt) REVERT: C 790 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8561 (mtmm) REVERT: C 820 ASP cc_start: 0.8071 (t0) cc_final: 0.7772 (m-30) REVERT: C 825 LYS cc_start: 0.8993 (tptt) cc_final: 0.8773 (tptt) REVERT: C 994 ASP cc_start: 0.8214 (t70) cc_final: 0.7946 (t0) REVERT: C 1037 SER cc_start: 0.9206 (t) cc_final: 0.8904 (p) outliers start: 79 outliers final: 56 residues processed: 624 average time/residue: 0.1771 time to fit residues: 175.3193 Evaluate side-chains 634 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 565 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 307 optimal weight: 0.5980 chunk 277 optimal weight: 0.7980 chunk 290 optimal weight: 0.8980 chunk 214 optimal weight: 0.0980 chunk 156 optimal weight: 0.0980 chunk 314 optimal weight: 1.9990 chunk 273 optimal weight: 0.0470 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 755 GLN B 777 ASN B1002 GLN B1119 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 969 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091730 restraints weight = 59227.759| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.32 r_work: 0.3283 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28173 Z= 0.143 Angle : 0.765 14.716 38538 Z= 0.356 Chirality : 0.046 0.641 4650 Planarity : 0.004 0.081 4761 Dihedral : 8.362 93.245 5945 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.07 % Favored : 94.74 % Rotamer: Outliers : 2.29 % Allowed : 19.27 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3273 helix: 1.66 (0.20), residues: 741 sheet: 0.16 (0.19), residues: 717 loop : -1.12 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 765 TYR 0.023 0.001 TYR A 495 PHE 0.024 0.001 PHE A 497 TRP 0.017 0.001 TRP C 104 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00314 (28014) covalent geometry : angle 0.72914 (38103) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.78373 ( 84) hydrogen bonds : bond 0.03763 ( 1084) hydrogen bonds : angle 5.79383 ( 2967) link_ALPHA1-4 : bond 0.01777 ( 27) link_ALPHA1-4 : angle 3.39588 ( 81) link_BETA1-4 : bond 0.00389 ( 33) link_BETA1-4 : angle 1.26100 ( 99) link_BETA1-6 : bond 0.01681 ( 3) link_BETA1-6 : angle 1.90981 ( 9) link_NAG-ASN : bond 0.00310 ( 54) link_NAG-ASN : angle 2.36423 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 586 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7906 (m) cc_final: 0.7672 (m) REVERT: B 52 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 96 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5656 (tt0) REVERT: B 99 ASN cc_start: 0.8397 (t0) cc_final: 0.8018 (t0) REVERT: B 140 PHE cc_start: 0.7887 (p90) cc_final: 0.7478 (p90) REVERT: B 153 MET cc_start: 0.6427 (tmm) cc_final: 0.6065 (tpt) REVERT: B 289 VAL cc_start: 0.8851 (t) cc_final: 0.8599 (m) REVERT: B 314 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8458 (mm-40) REVERT: B 360 ASN cc_start: 0.8651 (t0) cc_final: 0.8241 (t0) REVERT: B 383 SER cc_start: 0.8843 (t) cc_final: 0.8125 (m) REVERT: B 406 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 434 ILE cc_start: 0.8925 (mm) cc_final: 0.8646 (mm) REVERT: B 436 TRP cc_start: 0.7164 (p90) cc_final: 0.6727 (p90) REVERT: B 452 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7782 (ptm160) REVERT: B 460 ASN cc_start: 0.7852 (m-40) cc_final: 0.7539 (m110) REVERT: B 523 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8423 (p) REVERT: B 537 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8348 (ttpt) REVERT: B 557 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8589 (ptpt) REVERT: B 565 PHE cc_start: 0.7168 (m-10) cc_final: 0.6644 (m-10) REVERT: B 585 LEU cc_start: 0.8556 (mt) cc_final: 0.8299 (mt) REVERT: B 596 SER cc_start: 0.9221 (m) cc_final: 0.8673 (p) REVERT: B 642 VAL cc_start: 0.9343 (t) cc_final: 0.9083 (p) REVERT: B 650 LEU cc_start: 0.8376 (tp) cc_final: 0.8152 (tp) REVERT: B 762 GLN cc_start: 0.8584 (tt0) cc_final: 0.8378 (mt0) REVERT: B 815 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8457 (tpp80) REVERT: B 820 ASP cc_start: 0.8079 (t0) cc_final: 0.7865 (m-30) REVERT: B 825 LYS cc_start: 0.9030 (tptt) cc_final: 0.8801 (tptt) REVERT: B 912 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8417 (p) REVERT: B 918 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 990 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 1017 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 1107 ARG cc_start: 0.8715 (mtt90) cc_final: 0.8275 (mtt90) REVERT: A 153 MET cc_start: 0.6012 (tpt) cc_final: 0.5604 (ppp) REVERT: A 169 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 289 VAL cc_start: 0.8910 (t) cc_final: 0.8495 (m) REVERT: A 294 ASP cc_start: 0.8346 (p0) cc_final: 0.8074 (p0) REVERT: A 297 SER cc_start: 0.8733 (m) cc_final: 0.8382 (m) REVERT: A 324 GLU cc_start: 0.7991 (pm20) cc_final: 0.7617 (pm20) REVERT: A 357 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7636 (tpp-160) REVERT: A 360 ASN cc_start: 0.8672 (t0) cc_final: 0.8257 (t0) REVERT: A 406 GLU cc_start: 0.7951 (mp0) cc_final: 0.7584 (mp0) REVERT: A 456 PHE cc_start: 0.8223 (m-80) cc_final: 0.7994 (m-80) REVERT: A 523 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 557 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8635 (ptpt) REVERT: A 565 PHE cc_start: 0.7262 (m-10) cc_final: 0.6823 (m-80) REVERT: A 596 SER cc_start: 0.9280 (m) cc_final: 0.8772 (p) REVERT: A 633 TRP cc_start: 0.8715 (p-90) cc_final: 0.7908 (p-90) REVERT: A 725 GLU cc_start: 0.8359 (tt0) cc_final: 0.8059 (tt0) REVERT: A 790 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8777 (mtmm) REVERT: A 904 TYR cc_start: 0.8534 (m-10) cc_final: 0.8275 (m-10) REVERT: A 986 LYS cc_start: 0.8484 (ttpp) cc_final: 0.7965 (ttmm) REVERT: A 990 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 102 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7244 (mmt-90) REVERT: C 177 MET cc_start: 0.5530 (mpp) cc_final: 0.5243 (mpp) REVERT: C 188 ASN cc_start: 0.7658 (m-40) cc_final: 0.7067 (t0) REVERT: C 271 GLN cc_start: 0.8636 (mt0) cc_final: 0.8308 (mt0) REVERT: C 273 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7468 (mtt-85) REVERT: C 276 LEU cc_start: 0.9013 (tp) cc_final: 0.8805 (tt) REVERT: C 324 GLU cc_start: 0.8241 (pm20) cc_final: 0.7757 (pm20) REVERT: C 342 PHE cc_start: 0.8650 (m-80) cc_final: 0.8227 (m-80) REVERT: C 349 SER cc_start: 0.8091 (m) cc_final: 0.7812 (p) REVERT: C 370 ASN cc_start: 0.7540 (p0) cc_final: 0.7265 (m-40) REVERT: C 383 SER cc_start: 0.8849 (t) cc_final: 0.8340 (p) REVERT: C 406 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 434 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8636 (mm) REVERT: C 436 TRP cc_start: 0.7311 (p90) cc_final: 0.6936 (p90) REVERT: C 452 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7498 (ptm160) REVERT: C 453 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.6180 (p90) REVERT: C 456 PHE cc_start: 0.7771 (m-80) cc_final: 0.7423 (m-80) REVERT: C 495 TYR cc_start: 0.6566 (m-80) cc_final: 0.6261 (m-80) REVERT: C 523 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8483 (p) REVERT: C 565 PHE cc_start: 0.6945 (m-10) cc_final: 0.6430 (m-10) REVERT: C 587 ILE cc_start: 0.8812 (mt) cc_final: 0.8573 (tp) REVERT: C 633 TRP cc_start: 0.8492 (p-90) cc_final: 0.6931 (p-90) REVERT: C 663 ASP cc_start: 0.7974 (t0) cc_final: 0.7724 (t0) REVERT: C 737 ASP cc_start: 0.8011 (t0) cc_final: 0.7742 (t70) REVERT: C 776 LYS cc_start: 0.8655 (tptm) cc_final: 0.8313 (tmmt) REVERT: C 787 GLN cc_start: 0.8517 (mt0) cc_final: 0.8252 (mp10) REVERT: C 790 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8551 (mtmm) REVERT: C 820 ASP cc_start: 0.8090 (t0) cc_final: 0.7771 (m-30) REVERT: C 825 LYS cc_start: 0.8975 (tptt) cc_final: 0.8763 (tptt) REVERT: C 850 ILE cc_start: 0.7698 (mp) cc_final: 0.7451 (pt) REVERT: C 994 ASP cc_start: 0.8185 (t70) cc_final: 0.7914 (t0) REVERT: C 1037 SER cc_start: 0.9174 (t) cc_final: 0.8915 (p) outliers start: 66 outliers final: 48 residues processed: 617 average time/residue: 0.1752 time to fit residues: 171.3538 Evaluate side-chains 632 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 573 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 225 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 270 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 129 optimal weight: 0.0670 chunk 210 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 777 ASN B1002 GLN B1119 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 969 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 969 ASN C1113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.113006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090822 restraints weight = 59315.517| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.30 r_work: 0.3267 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28173 Z= 0.168 Angle : 0.769 14.722 38538 Z= 0.361 Chirality : 0.047 0.643 4650 Planarity : 0.004 0.060 4761 Dihedral : 8.033 90.901 5945 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.41 % Favored : 94.41 % Rotamer: Outliers : 2.36 % Allowed : 19.38 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3273 helix: 1.64 (0.20), residues: 741 sheet: 0.25 (0.19), residues: 684 loop : -1.16 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.027 0.002 TYR A 453 PHE 0.025 0.002 PHE C 140 TRP 0.017 0.001 TRP B 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00379 (28014) covalent geometry : angle 0.73148 (38103) SS BOND : bond 0.00594 ( 42) SS BOND : angle 2.03138 ( 84) hydrogen bonds : bond 0.03836 ( 1084) hydrogen bonds : angle 5.82661 ( 2967) link_ALPHA1-4 : bond 0.01748 ( 27) link_ALPHA1-4 : angle 3.44861 ( 81) link_BETA1-4 : bond 0.00359 ( 33) link_BETA1-4 : angle 1.28610 ( 99) link_BETA1-6 : bond 0.01451 ( 3) link_BETA1-6 : angle 1.57476 ( 9) link_NAG-ASN : bond 0.00291 ( 54) link_NAG-ASN : angle 2.37080 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6818.50 seconds wall clock time: 117 minutes 27.88 seconds (7047.88 seconds total)