Starting phenix.real_space_refine on Fri Mar 6 01:17:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1u_24123/03_2026/7n1u_24123_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1u_24123/03_2026/7n1u_24123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n1u_24123/03_2026/7n1u_24123_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1u_24123/03_2026/7n1u_24123_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n1u_24123/03_2026/7n1u_24123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1u_24123/03_2026/7n1u_24123.map" } resolution = 3.14 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= 0.043 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 114 5.16 5 C 16908 2.51 5 N 4299 2.21 5 O 5298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 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: 26619 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8421 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "B" Number of atoms: 8421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8421 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "C" Number of atoms: 8421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8421 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.33, per 1000 atoms: 0.24 Number of scatterers: 26619 At special positions: 0 Unit cell: (155.113, 155.938, 196.366, 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 114 16.00 O 5298 8.00 N 4299 7.00 C 16908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.78 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.81 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.01 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.90 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.78 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.89 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.99 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=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.57 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.58 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.65 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.75 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.94 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.97 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.85 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.60 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.06 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.70 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.64 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.54 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.42 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.66 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.98 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.74 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.34 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.10 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.68 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 M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 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 L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1403 " - " ASN A 331 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 48 sheets defined 27.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.711A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.061A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.725A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.453A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.691A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.567A 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 removed outlier: 3.717A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) 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: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.433A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1159 removed outlier: 3.756A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.267A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.538A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.962A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.342A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.632A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.728A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.529A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.603A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.646A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.518A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.549A 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 removed outlier: 3.570A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) 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: 3.795A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.538A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.004A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.726A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.116A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.774A 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 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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: 4.111A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.446A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.515A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.668A 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 removed outlier: 3.542A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.530A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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: 3.825A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.763A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.718A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.845A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.231A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.235A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.165A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.791A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.653A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.100A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.259A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.898A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.435A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.437A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.737A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.891A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.804A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.712A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.293A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.732A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.973A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.927A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.504A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.162A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.106A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.997A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.416A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.781A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.669A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.040A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.573A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.966A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.828A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.300A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.976A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.716A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.936A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.331A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.480A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3054 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: 6.81 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5292 1.33 - 1.45: 6726 1.45 - 1.58: 15042 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 27204 Sorted by residual: bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.543 -0.028 5.50e-03 3.31e+04 2.66e+01 bond pdb=" N CYS C 15 " pdb=" CA CYS C 15 " ideal model delta sigma weight residual 1.457 1.514 -0.057 1.23e-02 6.61e+03 2.12e+01 bond pdb=" C5 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.413 1.498 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.413 1.496 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 27199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 30194 2.31 - 4.62: 6316 4.62 - 6.94: 440 6.94 - 9.25: 36 9.25 - 11.56: 10 Bond angle restraints: 36996 Sorted by residual: angle pdb=" N ARG A1107 " pdb=" CA ARG A1107 " pdb=" C ARG A1107 " ideal model delta sigma weight residual 112.34 123.59 -11.25 1.30e+00 5.92e-01 7.49e+01 angle pdb=" OD1 ASN C1074 " pdb=" CG ASN C1074 " pdb=" ND2 ASN C1074 " ideal model delta sigma weight residual 122.60 114.21 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" OD1 ASN B1074 " pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 122.60 114.23 8.37 1.00e+00 1.00e+00 7.01e+01 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 112.34 123.12 -10.78 1.30e+00 5.92e-01 6.88e+01 angle pdb=" N ARG B 214 " pdb=" CA ARG B 214 " pdb=" C ARG B 214 " ideal model delta sigma weight residual 112.03 122.64 -10.61 1.31e+00 5.83e-01 6.56e+01 ... (remaining 36991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 16574 24.39 - 48.79: 692 48.79 - 73.18: 151 73.18 - 97.58: 43 97.58 - 121.97: 21 Dihedral angle restraints: 17481 sinusoidal: 8091 harmonic: 9390 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.06 85.06 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -165.40 79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -12.57 -73.43 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 17478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.616: 4444 0.616 - 1.232: 9 1.232 - 1.848: 3 1.848 - 2.464: 1 2.464 - 3.080: 1 Chirality restraints: 4458 Sorted by residual: chirality pdb=" C1 NAG B1403 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1403 " pdb=" O5 NAG B1403 " both_signs ideal model delta sigma weight residual False -2.40 0.68 -3.08 2.00e-01 2.50e+01 2.37e+02 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.49 -1.91 2.00e-01 2.50e+01 9.09e+01 chirality pdb=" C1 FUC W 3 " pdb=" O6 NAG W 1 " pdb=" C2 FUC W 3 " pdb=" O5 FUC W 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.84e+01 ... (remaining 4455 not shown) Planarity restraints: 4698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.319 2.00e-02 2.50e+03 3.28e-01 1.35e+03 pdb=" CG ASN B 343 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.553 2.00e-02 2.50e+03 pdb=" C1 NAG B1404 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.311 2.00e-02 2.50e+03 3.13e-01 1.23e+03 pdb=" CG ASN C 343 " 0.097 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.522 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " -0.334 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.069 2.00e-02 2.50e+03 2.28e-01 6.49e+02 pdb=" CG ASN C 61 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " -0.141 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.405 2.00e-02 2.50e+03 pdb=" C1 NAG C1401 " -0.258 2.00e-02 2.50e+03 ... (remaining 4695 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 83 2.58 - 3.16: 21422 3.16 - 3.74: 40140 3.74 - 4.32: 57496 4.32 - 4.90: 92987 Nonbonded interactions: 212128 Sorted by model distance: nonbonded pdb=" ND2 ASN B 234 " pdb=" C1 NAG R 1 " model vdw 2.003 3.550 nonbonded pdb=" ND2 ASN C 149 " pdb=" C1 NAG C1402 " model vdw 2.023 3.550 nonbonded pdb=" ND2 ASN C 149 " pdb=" O5 NAG C1402 " model vdw 2.030 3.120 nonbonded pdb=" CD ARG B 454 " pdb=" CD1 LEU B 492 " model vdw 2.037 3.860 nonbonded pdb=" ND2 ASN A 149 " pdb=" C1 NAG A1402 " model vdw 2.045 3.550 ... (remaining 212123 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = (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 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' 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) } 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: 8.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.870 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.026 0.960 27336 Z= 1.358 Angle : 2.062 46.504 37350 Z= 1.240 Chirality : 0.129 3.080 4458 Planarity : 0.012 0.122 4650 Dihedral : 14.945 121.970 11313 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.05 % Favored : 93.70 % Rotamer: Outliers : 1.56 % Allowed : 5.17 % Favored : 93.27 % Cbeta Deviations : 0.23 % 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: -1.65 (0.13), residues: 3189 helix: -1.36 (0.16), residues: 714 sheet: 0.24 (0.21), residues: 549 loop : -1.43 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 328 TYR 0.112 0.018 TYR A 495 PHE 0.101 0.013 PHE A 718 TRP 0.182 0.024 TRP A 258 HIS 0.017 0.004 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01347 (27204) covalent geometry : angle 1.76507 (36996) SS BOND : bond 0.53180 ( 42) SS BOND : angle 15.61669 ( 84) hydrogen bonds : bond 0.16230 ( 1092) hydrogen bonds : angle 8.64547 ( 3054) link_ALPHA1-4 : bond 0.01985 ( 6) link_ALPHA1-4 : angle 2.76464 ( 18) link_BETA1-4 : bond 0.01897 ( 33) link_BETA1-4 : angle 3.17796 ( 99) link_BETA1-6 : bond 0.03066 ( 3) link_BETA1-6 : angle 3.32952 ( 9) link_NAG-ASN : bond 0.21451 ( 48) link_NAG-ASN : angle 12.30812 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 757 time to evaluate : 0.990 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: A 54 LEU cc_start: 0.8501 (mt) cc_final: 0.8202 (mt) REVERT: A 125 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.7061 (p0) REVERT: A 133 PHE cc_start: 0.7142 (m-80) cc_final: 0.6872 (m-80) REVERT: A 140 PHE cc_start: 0.7790 (p90) cc_final: 0.7137 (p90) REVERT: A 188 ASN cc_start: 0.7844 (t0) cc_final: 0.7091 (t0) REVERT: A 205 SER cc_start: 0.8932 (p) cc_final: 0.8588 (t) REVERT: A 207 HIS cc_start: 0.7172 (t-170) cc_final: 0.6674 (t-90) REVERT: A 224 GLU cc_start: 0.7458 (mp0) cc_final: 0.7184 (mp0) REVERT: A 244 LEU cc_start: 0.5148 (mt) cc_final: 0.4649 (mt) REVERT: A 278 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8010 (ttmt) REVERT: A 286 THR cc_start: 0.8800 (m) cc_final: 0.8547 (p) REVERT: A 306 PHE cc_start: 0.8536 (m-80) cc_final: 0.8252 (m-80) REVERT: A 323 THR cc_start: 0.8759 (p) cc_final: 0.8453 (p) REVERT: A 324 GLU cc_start: 0.7492 (pm20) cc_final: 0.7039 (pm20) REVERT: A 391 CYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6094 (m) REVERT: A 392 PHE cc_start: 0.8375 (m-80) cc_final: 0.7954 (m-80) REVERT: A 425 LEU cc_start: 0.7736 (mt) cc_final: 0.7056 (mt) REVERT: A 555 SER cc_start: 0.7938 (t) cc_final: 0.7498 (t) REVERT: A 563 GLN cc_start: 0.7550 (mt0) cc_final: 0.7291 (mt0) REVERT: A 586 ASP cc_start: 0.7946 (m-30) cc_final: 0.7441 (m-30) REVERT: A 588 THR cc_start: 0.8762 (m) cc_final: 0.8469 (t) REVERT: A 664 ILE cc_start: 0.9118 (mt) cc_final: 0.8862 (mm) REVERT: A 776 LYS cc_start: 0.7976 (tmmt) cc_final: 0.7687 (ttpt) REVERT: A 780 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 816 SER cc_start: 0.8803 (p) cc_final: 0.8530 (p) REVERT: A 904 TYR cc_start: 0.7836 (m-10) cc_final: 0.7505 (m-80) REVERT: A 907 ASN cc_start: 0.8931 (t0) cc_final: 0.8679 (t0) REVERT: A 933 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8110 (mtpp) REVERT: A 945 LEU cc_start: 0.8738 (mm) cc_final: 0.8500 (mm) REVERT: A 957 GLN cc_start: 0.7659 (tt0) cc_final: 0.7451 (tt0) REVERT: A 986 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8187 (ttmm) REVERT: A 990 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 994 ASP cc_start: 0.7504 (t0) cc_final: 0.7150 (t0) REVERT: A 1102 TRP cc_start: 0.8842 (m100) cc_final: 0.8585 (m100) REVERT: B 99 ASN cc_start: 0.8308 (m-40) cc_final: 0.7951 (m-40) REVERT: B 137 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7507 (t0) REVERT: B 157 PHE cc_start: 0.7077 (p90) cc_final: 0.6691 (p90) REVERT: B 237 ARG cc_start: 0.7395 (ptt-90) cc_final: 0.7090 (ptt-90) REVERT: B 278 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8059 (ttmm) REVERT: B 306 PHE cc_start: 0.8740 (m-80) cc_final: 0.8457 (m-80) REVERT: B 309 GLU cc_start: 0.8035 (mp0) cc_final: 0.7569 (mp0) REVERT: B 360 ASN cc_start: 0.8085 (t0) cc_final: 0.7839 (t0) REVERT: B 428 ASP cc_start: 0.8179 (p0) cc_final: 0.7888 (p0) REVERT: B 541 PHE cc_start: 0.8723 (p90) cc_final: 0.8496 (p90) REVERT: B 560 LEU cc_start: 0.8446 (mp) cc_final: 0.8032 (mp) REVERT: B 563 GLN cc_start: 0.7470 (mt0) cc_final: 0.7262 (mt0) REVERT: B 565 PHE cc_start: 0.7626 (m-80) cc_final: 0.7338 (m-80) REVERT: B 586 ASP cc_start: 0.7835 (m-30) cc_final: 0.7396 (m-30) REVERT: B 619 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 646 ARG cc_start: 0.7720 (mmt180) cc_final: 0.7496 (mmm160) REVERT: B 776 LYS cc_start: 0.8534 (tppt) cc_final: 0.8300 (tppt) REVERT: B 816 SER cc_start: 0.8479 (p) cc_final: 0.8250 (p) REVERT: B 907 ASN cc_start: 0.8916 (t0) cc_final: 0.8672 (t0) REVERT: B 918 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 957 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 960 ASN cc_start: 0.8401 (t0) cc_final: 0.8103 (t0) REVERT: B 979 ASP cc_start: 0.7837 (t0) cc_final: 0.7526 (t0) REVERT: B 985 ASP cc_start: 0.7227 (p0) cc_final: 0.6775 (p0) REVERT: B 986 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8239 (tmtt) REVERT: B 994 ASP cc_start: 0.7534 (t0) cc_final: 0.7222 (t0) REVERT: C 39 PRO cc_start: 0.8865 (Cg_endo) cc_final: 0.8643 (Cg_exo) REVERT: C 40 ASP cc_start: 0.7998 (m-30) cc_final: 0.7780 (m-30) REVERT: C 54 LEU cc_start: 0.8485 (mt) cc_final: 0.8125 (mt) REVERT: C 133 PHE cc_start: 0.7241 (m-80) cc_final: 0.6715 (m-80) REVERT: C 179 LEU cc_start: 0.8324 (tp) cc_final: 0.8115 (tp) REVERT: C 190 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6970 (mmm-85) REVERT: C 195 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8227 (mtpt) REVERT: C 203 ILE cc_start: 0.8770 (mt) cc_final: 0.8277 (pt) REVERT: C 207 HIS cc_start: 0.7147 (t-90) cc_final: 0.6396 (t-90) REVERT: C 224 GLU cc_start: 0.7438 (mp0) cc_final: 0.7094 (mp0) REVERT: C 280 ASN cc_start: 0.8468 (p0) cc_final: 0.8027 (p0) REVERT: C 457 ARG cc_start: 0.6727 (tpm170) cc_final: 0.6318 (tpt90) REVERT: C 523 THR cc_start: 0.8244 (p) cc_final: 0.8041 (t) REVERT: C 563 GLN cc_start: 0.7721 (mt0) cc_final: 0.7416 (mt0) REVERT: C 584 ILE cc_start: 0.8282 (mm) cc_final: 0.7735 (mm) REVERT: C 588 THR cc_start: 0.8690 (m) cc_final: 0.8473 (t) REVERT: C 596 SER cc_start: 0.8919 (t) cc_final: 0.8654 (m) REVERT: C 619 GLU cc_start: 0.8161 (mp0) cc_final: 0.7710 (mp0) REVERT: C 654 GLU cc_start: 0.7522 (pt0) cc_final: 0.7245 (pt0) REVERT: C 664 ILE cc_start: 0.8878 (mp) cc_final: 0.8638 (mm) REVERT: C 936 ASP cc_start: 0.7903 (m-30) cc_final: 0.7685 (m-30) REVERT: C 985 ASP cc_start: 0.7255 (p0) cc_final: 0.6910 (p0) REVERT: C 990 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 1102 TRP cc_start: 0.8917 (m100) cc_final: 0.8654 (m100) REVERT: C 1127 ASP cc_start: 0.7619 (t70) cc_final: 0.7394 (t0) REVERT: C 1142 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7171 (tm-30) outliers start: 44 outliers final: 3 residues processed: 782 average time/residue: 0.1839 time to fit residues: 223.0861 Evaluate side-chains 618 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 612 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 318 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 234 ASN A 493 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 14 GLN B 30 ASN B 81 ASN B 188 ASN B 207 HIS B 394 ASN B 564 GLN B 580 GLN B 613 GLN B 751 ASN B 872 GLN B 926 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1119 ASN B1158 ASN C 115 GLN C 137 ASN C 149 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1088 HIS C1119 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083328 restraints weight = 63921.270| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.17 r_work: 0.3181 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27336 Z= 0.175 Angle : 0.899 22.595 37350 Z= 0.421 Chirality : 0.052 0.827 4458 Planarity : 0.004 0.052 4650 Dihedral : 10.774 110.283 5519 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.91 % Allowed : 9.92 % Favored : 88.17 % 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: -0.56 (0.14), residues: 3189 helix: 0.90 (0.19), residues: 711 sheet: -0.14 (0.18), residues: 672 loop : -0.98 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1091 TYR 0.029 0.002 TYR B 453 PHE 0.031 0.002 PHE C 565 TRP 0.018 0.002 TRP C 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00388 (27204) covalent geometry : angle 0.78664 (36996) SS BOND : bond 0.00612 ( 42) SS BOND : angle 2.39089 ( 84) hydrogen bonds : bond 0.04786 ( 1092) hydrogen bonds : angle 6.49373 ( 3054) link_ALPHA1-4 : bond 0.01330 ( 6) link_ALPHA1-4 : angle 2.16616 ( 18) link_BETA1-4 : bond 0.00483 ( 33) link_BETA1-4 : angle 2.01371 ( 99) link_BETA1-6 : bond 0.01231 ( 3) link_BETA1-6 : angle 2.16634 ( 9) link_NAG-ASN : bond 0.00848 ( 48) link_NAG-ASN : angle 6.60205 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 628 time to evaluate : 0.804 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: A 140 PHE cc_start: 0.8466 (p90) cc_final: 0.7982 (p90) REVERT: A 224 GLU cc_start: 0.8080 (mp0) cc_final: 0.7746 (mp0) REVERT: A 278 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8154 (ttmt) REVERT: A 306 PHE cc_start: 0.8716 (m-80) cc_final: 0.8487 (m-80) REVERT: A 323 THR cc_start: 0.8788 (p) cc_final: 0.8518 (p) REVERT: A 324 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: A 392 PHE cc_start: 0.8501 (m-80) cc_final: 0.8032 (m-80) REVERT: A 555 SER cc_start: 0.8073 (t) cc_final: 0.7377 (t) REVERT: A 586 ASP cc_start: 0.8065 (m-30) cc_final: 0.7579 (m-30) REVERT: A 599 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 664 ILE cc_start: 0.9057 (mt) cc_final: 0.8735 (mp) REVERT: A 675 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7092 (mt0) REVERT: A 780 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 796 ASP cc_start: 0.8281 (t0) cc_final: 0.8054 (t0) REVERT: A 816 SER cc_start: 0.8661 (p) cc_final: 0.8338 (p) REVERT: A 904 TYR cc_start: 0.8149 (m-10) cc_final: 0.7876 (m-80) REVERT: A 907 ASN cc_start: 0.9067 (t0) cc_final: 0.8753 (t0) REVERT: A 919 ASN cc_start: 0.9073 (m-40) cc_final: 0.8859 (m-40) REVERT: A 945 LEU cc_start: 0.8733 (mm) cc_final: 0.8444 (mm) REVERT: A 990 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 994 ASP cc_start: 0.8238 (t70) cc_final: 0.7767 (t0) REVERT: A 1092 GLU cc_start: 0.7913 (mp0) cc_final: 0.7673 (mp0) REVERT: A 1111 GLU cc_start: 0.8485 (pp20) cc_final: 0.8242 (pp20) REVERT: B 18 LEU cc_start: 0.7301 (mm) cc_final: 0.6573 (tp) REVERT: B 137 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7888 (t0) REVERT: B 191 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7803 (mp0) REVERT: B 224 GLU cc_start: 0.7963 (mp0) cc_final: 0.7760 (mp0) REVERT: B 278 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8306 (ttmm) REVERT: B 302 THR cc_start: 0.9210 (m) cc_final: 0.8747 (p) REVERT: B 442 ASP cc_start: 0.7215 (p0) cc_final: 0.6642 (p0) REVERT: B 559 PHE cc_start: 0.8099 (m-80) cc_final: 0.7841 (m-10) REVERT: B 560 LEU cc_start: 0.8420 (mp) cc_final: 0.8038 (mp) REVERT: B 586 ASP cc_start: 0.7889 (m-30) cc_final: 0.7561 (m-30) REVERT: B 776 LYS cc_start: 0.8773 (tppt) cc_final: 0.8502 (tppt) REVERT: B 907 ASN cc_start: 0.9100 (t0) cc_final: 0.8868 (t0) REVERT: B 957 GLN cc_start: 0.8232 (tm130) cc_final: 0.7906 (tm-30) REVERT: B 979 ASP cc_start: 0.8358 (t0) cc_final: 0.8049 (t0) REVERT: B 994 ASP cc_start: 0.8253 (t0) cc_final: 0.7745 (t0) REVERT: C 40 ASP cc_start: 0.8392 (m-30) cc_final: 0.8136 (m-30) REVERT: C 86 PHE cc_start: 0.8681 (t80) cc_final: 0.8383 (t80) REVERT: C 133 PHE cc_start: 0.7439 (m-80) cc_final: 0.6771 (m-80) REVERT: C 200 TYR cc_start: 0.5927 (m-80) cc_final: 0.5691 (m-80) REVERT: C 203 ILE cc_start: 0.8984 (mt) cc_final: 0.8524 (pt) REVERT: C 224 GLU cc_start: 0.7858 (mp0) cc_final: 0.7518 (mp0) REVERT: C 278 LYS cc_start: 0.8533 (tttm) cc_final: 0.8238 (ttpt) REVERT: C 280 ASN cc_start: 0.8581 (p0) cc_final: 0.8169 (p0) REVERT: C 281 GLU cc_start: 0.8094 (pm20) cc_final: 0.7891 (pm20) REVERT: C 355 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7469 (tpp-160) REVERT: C 555 SER cc_start: 0.8100 (t) cc_final: 0.7576 (m) REVERT: C 564 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6694 (tm-30) REVERT: C 584 ILE cc_start: 0.8418 (mm) cc_final: 0.7881 (mm) REVERT: C 619 GLU cc_start: 0.8399 (mp0) cc_final: 0.7899 (mp0) REVERT: C 654 GLU cc_start: 0.8355 (pt0) cc_final: 0.8068 (pt0) REVERT: C 773 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: C 823 PHE cc_start: 0.8311 (t80) cc_final: 0.8078 (t80) REVERT: C 918 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 936 ASP cc_start: 0.8176 (m-30) cc_final: 0.7894 (m-30) REVERT: C 990 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 1091 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8656 (ttm-80) outliers start: 54 outliers final: 25 residues processed: 650 average time/residue: 0.1731 time to fit residues: 175.9623 Evaluate side-chains 586 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 557 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 227 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 580 GLN A 935 GLN B 14 GLN B 23 GLN B 87 ASN B 188 ASN B 207 HIS B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN B1135 ASN C 196 ASN C 388 ASN C 762 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081692 restraints weight = 64924.798| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.21 r_work: 0.3159 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 27336 Z= 0.172 Angle : 0.814 20.360 37350 Z= 0.381 Chirality : 0.049 0.692 4458 Planarity : 0.004 0.045 4650 Dihedral : 9.939 106.744 5512 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.55 % Allowed : 12.54 % Favored : 84.91 % 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: -0.32 (0.14), residues: 3189 helix: 1.45 (0.20), residues: 711 sheet: -0.18 (0.18), residues: 654 loop : -0.91 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 577 TYR 0.024 0.002 TYR C1067 PHE 0.023 0.002 PHE B 565 TRP 0.010 0.002 TRP C 436 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00387 (27204) covalent geometry : angle 0.72009 (36996) SS BOND : bond 0.00555 ( 42) SS BOND : angle 3.02696 ( 84) hydrogen bonds : bond 0.04317 ( 1092) hydrogen bonds : angle 6.09184 ( 3054) link_ALPHA1-4 : bond 0.01339 ( 6) link_ALPHA1-4 : angle 2.42016 ( 18) link_BETA1-4 : bond 0.00451 ( 33) link_BETA1-4 : angle 1.81312 ( 99) link_BETA1-6 : bond 0.01358 ( 3) link_BETA1-6 : angle 2.28237 ( 9) link_NAG-ASN : bond 0.00649 ( 48) link_NAG-ASN : angle 5.48600 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 604 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8220 (t) REVERT: A 140 PHE cc_start: 0.8555 (p90) cc_final: 0.8168 (p90) REVERT: A 190 ARG cc_start: 0.7970 (mpt-90) cc_final: 0.7630 (mpt-90) REVERT: A 224 GLU cc_start: 0.8128 (mp0) cc_final: 0.7818 (mp0) REVERT: A 237 ARG cc_start: 0.8450 (ttp-170) cc_final: 0.7989 (ttp80) REVERT: A 278 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8344 (ttmt) REVERT: A 286 THR cc_start: 0.9026 (m) cc_final: 0.8602 (p) REVERT: A 287 ASP cc_start: 0.8370 (m-30) cc_final: 0.8016 (m-30) REVERT: A 290 ASP cc_start: 0.8197 (t0) cc_final: 0.7955 (t70) REVERT: A 291 CYS cc_start: 0.7564 (t) cc_final: 0.7198 (t) REVERT: A 323 THR cc_start: 0.8809 (p) cc_final: 0.8566 (p) REVERT: A 324 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: A 555 SER cc_start: 0.7987 (t) cc_final: 0.7109 (t) REVERT: A 563 GLN cc_start: 0.7793 (mt0) cc_final: 0.7472 (mt0) REVERT: A 586 ASP cc_start: 0.8011 (m-30) cc_final: 0.7414 (m-30) REVERT: A 599 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 619 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 675 GLN cc_start: 0.7403 (mm-40) cc_final: 0.7043 (mt0) REVERT: A 773 GLU cc_start: 0.8335 (tp30) cc_final: 0.8076 (tp30) REVERT: A 780 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 796 ASP cc_start: 0.8374 (t0) cc_final: 0.8129 (t0) REVERT: A 816 SER cc_start: 0.8838 (p) cc_final: 0.8544 (p) REVERT: A 904 TYR cc_start: 0.8184 (m-10) cc_final: 0.7862 (m-80) REVERT: A 907 ASN cc_start: 0.9076 (t0) cc_final: 0.8771 (t0) REVERT: A 919 ASN cc_start: 0.8996 (m-40) cc_final: 0.8687 (m-40) REVERT: A 945 LEU cc_start: 0.8713 (mm) cc_final: 0.8476 (mm) REVERT: A 1019 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7897 (ttp-110) REVERT: A 1041 ASP cc_start: 0.8569 (t70) cc_final: 0.8235 (t0) REVERT: A 1045 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8445 (tppt) REVERT: A 1092 GLU cc_start: 0.7949 (mp0) cc_final: 0.7742 (mp0) REVERT: A 1111 GLU cc_start: 0.8468 (pp20) cc_final: 0.8055 (pp20) REVERT: B 18 LEU cc_start: 0.7339 (mm) cc_final: 0.6696 (tp) REVERT: B 137 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7865 (t0) REVERT: B 191 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7784 (mp0) REVERT: B 223 LEU cc_start: 0.8680 (mt) cc_final: 0.8443 (mt) REVERT: B 224 GLU cc_start: 0.7984 (mp0) cc_final: 0.7764 (mp0) REVERT: B 269 TYR cc_start: 0.8086 (m-10) cc_final: 0.7842 (m-10) REVERT: B 278 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8299 (ttmm) REVERT: B 302 THR cc_start: 0.9231 (m) cc_final: 0.8766 (p) REVERT: B 360 ASN cc_start: 0.8524 (t0) cc_final: 0.8175 (t0) REVERT: B 414 GLN cc_start: 0.6733 (tp-100) cc_final: 0.6501 (tp40) REVERT: B 428 ASP cc_start: 0.8215 (p0) cc_final: 0.7949 (p0) REVERT: B 442 ASP cc_start: 0.7223 (p0) cc_final: 0.6795 (p0) REVERT: B 453 TYR cc_start: 0.7484 (p90) cc_final: 0.7098 (p90) REVERT: B 560 LEU cc_start: 0.8603 (mp) cc_final: 0.8397 (mp) REVERT: B 565 PHE cc_start: 0.7274 (m-80) cc_final: 0.6859 (m-80) REVERT: B 586 ASP cc_start: 0.7885 (m-30) cc_final: 0.7440 (m-30) REVERT: B 619 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8086 (mp0) REVERT: B 661 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 776 LYS cc_start: 0.8810 (tppt) cc_final: 0.8578 (tppt) REVERT: B 907 ASN cc_start: 0.9111 (t0) cc_final: 0.8883 (t0) REVERT: B 957 GLN cc_start: 0.8130 (tm130) cc_final: 0.7804 (tm-30) REVERT: B 979 ASP cc_start: 0.8305 (t0) cc_final: 0.8015 (t0) REVERT: C 40 ASP cc_start: 0.8320 (m-30) cc_final: 0.8087 (m-30) REVERT: C 86 PHE cc_start: 0.8721 (t80) cc_final: 0.8496 (t80) REVERT: C 133 PHE cc_start: 0.7458 (m-80) cc_final: 0.6687 (m-80) REVERT: C 188 ASN cc_start: 0.7186 (t0) cc_final: 0.6538 (t0) REVERT: C 190 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7226 (mmm-85) REVERT: C 207 HIS cc_start: 0.7331 (t-90) cc_final: 0.6978 (t-90) REVERT: C 224 GLU cc_start: 0.7972 (mp0) cc_final: 0.7571 (mp0) REVERT: C 280 ASN cc_start: 0.8590 (p0) cc_final: 0.8342 (p0) REVERT: C 281 GLU cc_start: 0.8276 (pm20) cc_final: 0.8041 (pm20) REVERT: C 409 GLN cc_start: 0.8117 (mt0) cc_final: 0.7786 (mt0) REVERT: C 555 SER cc_start: 0.7986 (t) cc_final: 0.7686 (m) REVERT: C 564 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6700 (tm-30) REVERT: C 584 ILE cc_start: 0.8494 (mm) cc_final: 0.8079 (mm) REVERT: C 654 GLU cc_start: 0.8336 (pt0) cc_final: 0.8026 (pt0) REVERT: C 661 GLU cc_start: 0.8161 (tt0) cc_final: 0.7847 (tm-30) REVERT: C 748 GLU cc_start: 0.8397 (mp0) cc_final: 0.8081 (pm20) REVERT: C 773 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: C 808 ASP cc_start: 0.7808 (t0) cc_final: 0.7319 (t0) REVERT: C 823 PHE cc_start: 0.8319 (t80) cc_final: 0.8088 (t80) REVERT: C 936 ASP cc_start: 0.8202 (m-30) cc_final: 0.7887 (m-30) REVERT: C 981 LEU cc_start: 0.8976 (mt) cc_final: 0.8761 (mt) REVERT: C 990 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8295 (mm-30) REVERT: C 1091 ARG cc_start: 0.8843 (mtp85) cc_final: 0.8627 (ttm-80) outliers start: 72 outliers final: 40 residues processed: 641 average time/residue: 0.1770 time to fit residues: 177.5630 Evaluate side-chains 600 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 555 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 84 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 34 optimal weight: 0.1980 chunk 220 optimal weight: 0.0170 chunk 180 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 207 HIS B 394 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 481 ASN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081126 restraints weight = 64856.668| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.16 r_work: 0.3138 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 27336 Z= 0.216 Angle : 0.820 18.545 37350 Z= 0.384 Chirality : 0.049 0.638 4458 Planarity : 0.004 0.046 4650 Dihedral : 9.665 106.553 5512 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.98 % Allowed : 14.28 % Favored : 82.75 % 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: -0.26 (0.14), residues: 3189 helix: 1.67 (0.20), residues: 687 sheet: -0.21 (0.18), residues: 672 loop : -0.89 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.024 0.002 TYR C1067 PHE 0.027 0.002 PHE B 565 TRP 0.010 0.001 TRP B 258 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00491 (27204) covalent geometry : angle 0.73642 (36996) SS BOND : bond 0.00453 ( 42) SS BOND : angle 3.33538 ( 84) hydrogen bonds : bond 0.04243 ( 1092) hydrogen bonds : angle 6.00256 ( 3054) link_ALPHA1-4 : bond 0.01277 ( 6) link_ALPHA1-4 : angle 2.50064 ( 18) link_BETA1-4 : bond 0.00388 ( 33) link_BETA1-4 : angle 1.78256 ( 99) link_BETA1-6 : bond 0.01296 ( 3) link_BETA1-6 : angle 2.48204 ( 9) link_NAG-ASN : bond 0.00569 ( 48) link_NAG-ASN : angle 5.03125 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 583 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8004 (t) REVERT: A 106 PHE cc_start: 0.7624 (m-80) cc_final: 0.7371 (m-80) REVERT: A 140 PHE cc_start: 0.8568 (p90) cc_final: 0.8308 (p90) REVERT: A 202 LYS cc_start: 0.9012 (mptt) cc_final: 0.8766 (mptt) REVERT: A 224 GLU cc_start: 0.8216 (mp0) cc_final: 0.7903 (mp0) REVERT: A 237 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8013 (ttp-170) REVERT: A 278 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8366 (ttmt) REVERT: A 286 THR cc_start: 0.9010 (m) cc_final: 0.8551 (p) REVERT: A 287 ASP cc_start: 0.8416 (m-30) cc_final: 0.8089 (m-30) REVERT: A 290 ASP cc_start: 0.8230 (t0) cc_final: 0.7959 (t70) REVERT: A 324 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: A 429 PHE cc_start: 0.8487 (t80) cc_final: 0.8173 (t80) REVERT: A 563 GLN cc_start: 0.7847 (mt0) cc_final: 0.7463 (mt0) REVERT: A 586 ASP cc_start: 0.7948 (m-30) cc_final: 0.7577 (m-30) REVERT: A 599 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (p) REVERT: A 675 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7059 (mt0) REVERT: A 697 MET cc_start: 0.8499 (ptm) cc_final: 0.8295 (ptm) REVERT: A 773 GLU cc_start: 0.8327 (tp30) cc_final: 0.8104 (tp30) REVERT: A 780 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 796 ASP cc_start: 0.8383 (t0) cc_final: 0.8138 (t0) REVERT: A 816 SER cc_start: 0.8871 (p) cc_final: 0.8651 (p) REVERT: A 819 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 904 TYR cc_start: 0.8193 (m-10) cc_final: 0.7875 (m-80) REVERT: A 907 ASN cc_start: 0.9086 (t0) cc_final: 0.8782 (t0) REVERT: A 994 ASP cc_start: 0.8438 (t70) cc_final: 0.7886 (t0) REVERT: A 1092 GLU cc_start: 0.7938 (mp0) cc_final: 0.7737 (mp0) REVERT: B 18 LEU cc_start: 0.7474 (mm) cc_final: 0.6826 (tp) REVERT: B 191 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7770 (mp0) REVERT: B 223 LEU cc_start: 0.8673 (mt) cc_final: 0.8439 (mt) REVERT: B 224 GLU cc_start: 0.7962 (mp0) cc_final: 0.7731 (mp0) REVERT: B 278 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8331 (ttmm) REVERT: B 302 THR cc_start: 0.9226 (m) cc_final: 0.8758 (p) REVERT: B 310 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8858 (tttp) REVERT: B 408 ARG cc_start: 0.8198 (ppt170) cc_final: 0.7509 (ppt170) REVERT: B 414 GLN cc_start: 0.6657 (tp-100) cc_final: 0.5645 (tp-100) REVERT: B 428 ASP cc_start: 0.8238 (p0) cc_final: 0.8020 (p0) REVERT: B 442 ASP cc_start: 0.7254 (p0) cc_final: 0.6888 (p0) REVERT: B 560 LEU cc_start: 0.8552 (mp) cc_final: 0.8335 (mp) REVERT: B 586 ASP cc_start: 0.7875 (m-30) cc_final: 0.7409 (m-30) REVERT: B 619 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8082 (mp0) REVERT: B 644 GLN cc_start: 0.8577 (tp40) cc_final: 0.8110 (tp40) REVERT: B 773 GLU cc_start: 0.8200 (tp30) cc_final: 0.7960 (tp30) REVERT: B 907 ASN cc_start: 0.9127 (t0) cc_final: 0.8895 (t0) REVERT: B 957 GLN cc_start: 0.8136 (tm130) cc_final: 0.7809 (tm-30) REVERT: B 979 ASP cc_start: 0.8310 (t0) cc_final: 0.8025 (t0) REVERT: C 40 ASP cc_start: 0.8297 (m-30) cc_final: 0.8063 (m-30) REVERT: C 188 ASN cc_start: 0.7060 (t0) cc_final: 0.6405 (t0) REVERT: C 190 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7242 (mmm-85) REVERT: C 207 HIS cc_start: 0.7297 (t-90) cc_final: 0.7003 (t-90) REVERT: C 224 GLU cc_start: 0.8001 (mp0) cc_final: 0.7620 (mp0) REVERT: C 409 GLN cc_start: 0.8188 (mt0) cc_final: 0.7967 (mt0) REVERT: C 437 ASN cc_start: 0.6585 (m-40) cc_final: 0.6353 (m-40) REVERT: C 450 ASN cc_start: 0.6138 (OUTLIER) cc_final: 0.5897 (p0) REVERT: C 555 SER cc_start: 0.7960 (t) cc_final: 0.7639 (m) REVERT: C 564 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6742 (tm-30) REVERT: C 568 ASP cc_start: 0.7848 (t70) cc_final: 0.7470 (p0) REVERT: C 619 GLU cc_start: 0.8153 (mp0) cc_final: 0.7459 (mp0) REVERT: C 654 GLU cc_start: 0.8358 (pt0) cc_final: 0.8064 (pt0) REVERT: C 773 GLU cc_start: 0.7922 (pt0) cc_final: 0.7671 (tt0) REVERT: C 808 ASP cc_start: 0.7796 (t0) cc_final: 0.7259 (t0) REVERT: C 936 ASP cc_start: 0.8203 (m-30) cc_final: 0.7879 (m-30) REVERT: C 990 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8239 (mm-30) outliers start: 84 outliers final: 53 residues processed: 629 average time/residue: 0.1715 time to fit residues: 169.6544 Evaluate side-chains 614 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 556 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 261 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 316 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 207 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.099831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081616 restraints weight = 64932.160| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.16 r_work: 0.3146 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27336 Z= 0.178 Angle : 0.776 16.591 37350 Z= 0.362 Chirality : 0.048 0.591 4458 Planarity : 0.004 0.045 4650 Dihedral : 9.011 105.872 5512 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.37 % Allowed : 15.30 % Favored : 81.33 % 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: -0.19 (0.14), residues: 3189 helix: 1.80 (0.20), residues: 687 sheet: -0.28 (0.18), residues: 687 loop : -0.82 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 102 TYR 0.023 0.001 TYR C1067 PHE 0.043 0.002 PHE B 157 TRP 0.015 0.001 TRP B 353 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00400 (27204) covalent geometry : angle 0.70732 (36996) SS BOND : bond 0.00428 ( 42) SS BOND : angle 2.47129 ( 84) hydrogen bonds : bond 0.03984 ( 1092) hydrogen bonds : angle 5.88629 ( 3054) link_ALPHA1-4 : bond 0.01401 ( 6) link_ALPHA1-4 : angle 2.55022 ( 18) link_BETA1-4 : bond 0.00428 ( 33) link_BETA1-4 : angle 1.65211 ( 99) link_BETA1-6 : bond 0.01818 ( 3) link_BETA1-6 : angle 2.18083 ( 9) link_NAG-ASN : bond 0.00551 ( 48) link_NAG-ASN : angle 4.58222 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 583 time to evaluate : 0.778 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: A 129 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8195 (mmpt) REVERT: A 140 PHE cc_start: 0.8608 (p90) cc_final: 0.8312 (p90) REVERT: A 191 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: A 224 GLU cc_start: 0.8230 (mp0) cc_final: 0.7930 (mp0) REVERT: A 237 ARG cc_start: 0.8372 (ttp-170) cc_final: 0.8080 (ttp80) REVERT: A 278 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8357 (ttmt) REVERT: A 286 THR cc_start: 0.8967 (m) cc_final: 0.8540 (p) REVERT: A 324 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: A 429 PHE cc_start: 0.8506 (t80) cc_final: 0.8179 (t80) REVERT: A 563 GLN cc_start: 0.7856 (mt0) cc_final: 0.7487 (mt0) REVERT: A 586 ASP cc_start: 0.7962 (m-30) cc_final: 0.7532 (m-30) REVERT: A 599 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 675 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7123 (mt0) REVERT: A 773 GLU cc_start: 0.8332 (tp30) cc_final: 0.8103 (tp30) REVERT: A 780 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 796 ASP cc_start: 0.8400 (t0) cc_final: 0.8136 (t0) REVERT: A 819 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 904 TYR cc_start: 0.8179 (m-10) cc_final: 0.7844 (m-80) REVERT: A 907 ASN cc_start: 0.9065 (t0) cc_final: 0.8769 (t0) REVERT: A 912 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 994 ASP cc_start: 0.8485 (t70) cc_final: 0.7904 (t0) REVERT: B 18 LEU cc_start: 0.7503 (mm) cc_final: 0.6891 (tp) REVERT: B 191 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7743 (mp0) REVERT: B 224 GLU cc_start: 0.7972 (mp0) cc_final: 0.7716 (mp0) REVERT: B 269 TYR cc_start: 0.8099 (m-10) cc_final: 0.7786 (m-80) REVERT: B 278 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8314 (ttmm) REVERT: B 310 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8786 (tttp) REVERT: B 408 ARG cc_start: 0.8262 (ppt170) cc_final: 0.7640 (ppt170) REVERT: B 414 GLN cc_start: 0.6511 (tp-100) cc_final: 0.5510 (tp-100) REVERT: B 560 LEU cc_start: 0.8580 (mp) cc_final: 0.8366 (mp) REVERT: B 586 ASP cc_start: 0.7854 (m-30) cc_final: 0.7387 (m-30) REVERT: B 619 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8093 (mp0) REVERT: B 644 GLN cc_start: 0.8582 (tp40) cc_final: 0.8084 (tp40) REVERT: B 773 GLU cc_start: 0.8216 (tp30) cc_final: 0.7976 (tp30) REVERT: B 776 LYS cc_start: 0.8828 (tppt) cc_final: 0.8466 (tttm) REVERT: B 825 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8282 (ttmm) REVERT: B 907 ASN cc_start: 0.9120 (t0) cc_final: 0.8884 (t0) REVERT: B 957 GLN cc_start: 0.8063 (tm130) cc_final: 0.7748 (tm-30) REVERT: B 979 ASP cc_start: 0.8295 (t0) cc_final: 0.8010 (t0) REVERT: C 40 ASP cc_start: 0.8292 (m-30) cc_final: 0.8086 (m-30) REVERT: C 177 MET cc_start: 0.3886 (ppp) cc_final: 0.3075 (ppp) REVERT: C 188 ASN cc_start: 0.7066 (t0) cc_final: 0.6357 (t0) REVERT: C 190 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.7205 (mmm-85) REVERT: C 207 HIS cc_start: 0.7474 (t-90) cc_final: 0.7151 (t-90) REVERT: C 224 GLU cc_start: 0.8033 (mp0) cc_final: 0.7686 (mp0) REVERT: C 269 TYR cc_start: 0.8031 (m-10) cc_final: 0.7717 (m-80) REVERT: C 280 ASN cc_start: 0.8760 (p0) cc_final: 0.8502 (p0) REVERT: C 281 GLU cc_start: 0.8543 (pm20) cc_final: 0.8334 (pm20) REVERT: C 409 GLN cc_start: 0.8158 (mt0) cc_final: 0.7469 (mp10) REVERT: C 437 ASN cc_start: 0.6622 (m-40) cc_final: 0.6374 (m-40) REVERT: C 442 ASP cc_start: 0.7649 (p0) cc_final: 0.7426 (p0) REVERT: C 450 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5965 (p0) REVERT: C 564 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6800 (tm-30) REVERT: C 568 ASP cc_start: 0.7828 (t70) cc_final: 0.7472 (p0) REVERT: C 584 ILE cc_start: 0.8518 (mm) cc_final: 0.8074 (mm) REVERT: C 654 GLU cc_start: 0.8380 (pt0) cc_final: 0.8092 (pt0) REVERT: C 808 ASP cc_start: 0.7806 (t0) cc_final: 0.7265 (t0) REVERT: C 904 TYR cc_start: 0.8214 (m-80) cc_final: 0.7904 (m-10) REVERT: C 936 ASP cc_start: 0.8204 (m-30) cc_final: 0.7892 (m-30) REVERT: C 981 LEU cc_start: 0.8968 (mt) cc_final: 0.8320 (mt) REVERT: C 983 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8188 (mtp180) REVERT: C 990 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8224 (mm-30) outliers start: 95 outliers final: 58 residues processed: 632 average time/residue: 0.1693 time to fit residues: 168.1757 Evaluate side-chains 618 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 553 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 31 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 150 optimal weight: 0.0060 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 285 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 388 ASN C 519 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.100567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082285 restraints weight = 64535.577| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.17 r_work: 0.3163 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27336 Z= 0.149 Angle : 0.753 15.744 37350 Z= 0.351 Chirality : 0.047 0.559 4458 Planarity : 0.004 0.049 4650 Dihedral : 8.479 104.478 5510 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.90 % Allowed : 16.15 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.10 (0.14), residues: 3189 helix: 1.90 (0.20), residues: 687 sheet: -0.16 (0.18), residues: 702 loop : -0.81 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.021 0.001 TYR C1067 PHE 0.029 0.001 PHE C 133 TRP 0.019 0.001 TRP B 353 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00332 (27204) covalent geometry : angle 0.68596 (36996) SS BOND : bond 0.00715 ( 42) SS BOND : angle 2.60840 ( 84) hydrogen bonds : bond 0.03843 ( 1092) hydrogen bonds : angle 5.85138 ( 3054) link_ALPHA1-4 : bond 0.01494 ( 6) link_ALPHA1-4 : angle 2.67390 ( 18) link_BETA1-4 : bond 0.00422 ( 33) link_BETA1-4 : angle 1.57602 ( 99) link_BETA1-6 : bond 0.01824 ( 3) link_BETA1-6 : angle 1.93234 ( 9) link_NAG-ASN : bond 0.00540 ( 48) link_NAG-ASN : angle 4.38506 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 579 time to evaluate : 0.895 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: A 106 PHE cc_start: 0.7635 (m-80) cc_final: 0.7404 (m-80) REVERT: A 140 PHE cc_start: 0.8567 (p90) cc_final: 0.8290 (p90) REVERT: A 190 ARG cc_start: 0.8003 (mpt-90) cc_final: 0.7651 (mpt-90) REVERT: A 202 LYS cc_start: 0.9025 (mptt) cc_final: 0.8776 (mppt) REVERT: A 224 GLU cc_start: 0.8203 (mp0) cc_final: 0.7932 (mp0) REVERT: A 237 ARG cc_start: 0.8305 (ttp-170) cc_final: 0.8084 (ttp80) REVERT: A 278 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8343 (ttmt) REVERT: A 286 THR cc_start: 0.8915 (m) cc_final: 0.8630 (p) REVERT: A 324 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 374 PHE cc_start: 0.8055 (m-80) cc_final: 0.7764 (m-80) REVERT: A 392 PHE cc_start: 0.8537 (m-80) cc_final: 0.8228 (m-80) REVERT: A 429 PHE cc_start: 0.8494 (t80) cc_final: 0.8146 (t80) REVERT: A 563 GLN cc_start: 0.7785 (mt0) cc_final: 0.7442 (mt0) REVERT: A 586 ASP cc_start: 0.7976 (m-30) cc_final: 0.7536 (m-30) REVERT: A 599 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 675 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7109 (mt0) REVERT: A 773 GLU cc_start: 0.8314 (tp30) cc_final: 0.8047 (tp30) REVERT: A 776 LYS cc_start: 0.8783 (tppp) cc_final: 0.8338 (ttpt) REVERT: A 796 ASP cc_start: 0.8382 (t0) cc_final: 0.8124 (t0) REVERT: A 904 TYR cc_start: 0.8143 (m-10) cc_final: 0.7806 (m-80) REVERT: A 907 ASN cc_start: 0.9040 (t0) cc_final: 0.8749 (t0) REVERT: A 912 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 983 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8155 (mtp180) REVERT: A 994 ASP cc_start: 0.8453 (t70) cc_final: 0.7871 (t0) REVERT: A 1102 TRP cc_start: 0.8889 (m100) cc_final: 0.8444 (m100) REVERT: B 18 LEU cc_start: 0.7428 (mm) cc_final: 0.6872 (tp) REVERT: B 137 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7481 (t0) REVERT: B 191 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7671 (mp0) REVERT: B 223 LEU cc_start: 0.8593 (mt) cc_final: 0.8378 (mt) REVERT: B 224 GLU cc_start: 0.7942 (mp0) cc_final: 0.7720 (mp0) REVERT: B 269 TYR cc_start: 0.8051 (m-10) cc_final: 0.7828 (m-80) REVERT: B 278 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8280 (ttmm) REVERT: B 353 TRP cc_start: 0.7004 (p-90) cc_final: 0.6744 (p-90) REVERT: B 408 ARG cc_start: 0.8230 (ppt170) cc_final: 0.7612 (ppt170) REVERT: B 414 GLN cc_start: 0.6506 (tp-100) cc_final: 0.5608 (tp-100) REVERT: B 442 ASP cc_start: 0.7187 (p0) cc_final: 0.6815 (p0) REVERT: B 586 ASP cc_start: 0.7834 (m-30) cc_final: 0.7370 (m-30) REVERT: B 619 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8044 (mp0) REVERT: B 773 GLU cc_start: 0.8204 (tp30) cc_final: 0.7955 (tp30) REVERT: B 825 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8317 (ttmm) REVERT: B 907 ASN cc_start: 0.9103 (t0) cc_final: 0.8867 (t0) REVERT: B 957 GLN cc_start: 0.8025 (tm130) cc_final: 0.7709 (tm-30) REVERT: B 979 ASP cc_start: 0.8289 (t0) cc_final: 0.8005 (t0) REVERT: C 177 MET cc_start: 0.3807 (ppp) cc_final: 0.2990 (ppp) REVERT: C 188 ASN cc_start: 0.7016 (t0) cc_final: 0.6322 (t0) REVERT: C 190 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7245 (mmm-85) REVERT: C 203 ILE cc_start: 0.8870 (mp) cc_final: 0.8458 (pt) REVERT: C 207 HIS cc_start: 0.7459 (t-90) cc_final: 0.7227 (t-90) REVERT: C 224 GLU cc_start: 0.8016 (mp0) cc_final: 0.7685 (mp0) REVERT: C 280 ASN cc_start: 0.8727 (p0) cc_final: 0.8441 (p0) REVERT: C 319 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8090 (mtp-110) REVERT: C 409 GLN cc_start: 0.8109 (mt0) cc_final: 0.7485 (mp10) REVERT: C 564 GLN cc_start: 0.7404 (tm-30) cc_final: 0.7090 (tm-30) REVERT: C 568 ASP cc_start: 0.7830 (t70) cc_final: 0.7478 (p0) REVERT: C 654 GLU cc_start: 0.8383 (pt0) cc_final: 0.8091 (pt0) REVERT: C 776 LYS cc_start: 0.8845 (tppp) cc_final: 0.8600 (tptp) REVERT: C 808 ASP cc_start: 0.7823 (t0) cc_final: 0.7280 (t0) REVERT: C 904 TYR cc_start: 0.8182 (m-80) cc_final: 0.7903 (m-10) REVERT: C 912 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8622 (p) REVERT: C 936 ASP cc_start: 0.8189 (m-30) cc_final: 0.7878 (m-30) REVERT: C 983 ARG cc_start: 0.8392 (mtp180) cc_final: 0.8189 (mtp180) REVERT: C 990 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8165 (mm-30) REVERT: C 1004 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8473 (tt) outliers start: 82 outliers final: 53 residues processed: 622 average time/residue: 0.1801 time to fit residues: 175.8469 Evaluate side-chains 605 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 545 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 59 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 316 optimal weight: 0.0980 chunk 106 optimal weight: 0.4980 chunk 309 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 935 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 188 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 388 ASN C 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080879 restraints weight = 64543.605| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.19 r_work: 0.3140 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 27336 Z= 0.206 Angle : 0.781 15.316 37350 Z= 0.367 Chirality : 0.048 0.550 4458 Planarity : 0.004 0.047 4650 Dihedral : 8.442 105.334 5510 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.37 % Allowed : 16.79 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3189 helix: 1.81 (0.20), residues: 687 sheet: -0.25 (0.18), residues: 684 loop : -0.85 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.023 0.002 TYR C1067 PHE 0.028 0.002 PHE C 157 TRP 0.020 0.001 TRP C 152 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00470 (27204) covalent geometry : angle 0.71646 (36996) SS BOND : bond 0.00464 ( 42) SS BOND : angle 2.66910 ( 84) hydrogen bonds : bond 0.04024 ( 1092) hydrogen bonds : angle 5.87053 ( 3054) link_ALPHA1-4 : bond 0.01433 ( 6) link_ALPHA1-4 : angle 2.77163 ( 18) link_BETA1-4 : bond 0.00384 ( 33) link_BETA1-4 : angle 1.66275 ( 99) link_BETA1-6 : bond 0.01506 ( 3) link_BETA1-6 : angle 1.66520 ( 9) link_NAG-ASN : bond 0.00523 ( 48) link_NAG-ASN : angle 4.37918 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 566 time to evaluate : 1.007 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: A 140 PHE cc_start: 0.8634 (p90) cc_final: 0.8369 (p90) REVERT: A 190 ARG cc_start: 0.8040 (mpt-90) cc_final: 0.7660 (mpt-90) REVERT: A 191 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: A 202 LYS cc_start: 0.9004 (mptt) cc_final: 0.8567 (mppt) REVERT: A 224 GLU cc_start: 0.8219 (mp0) cc_final: 0.7957 (mp0) REVERT: A 237 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8198 (ttp80) REVERT: A 278 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8450 (ttmt) REVERT: A 324 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: A 429 PHE cc_start: 0.8496 (t80) cc_final: 0.8151 (t80) REVERT: A 563 GLN cc_start: 0.7809 (mt0) cc_final: 0.7430 (mt0) REVERT: A 586 ASP cc_start: 0.7987 (m-30) cc_final: 0.7552 (m-30) REVERT: A 599 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8756 (p) REVERT: A 675 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7124 (mt0) REVERT: A 773 GLU cc_start: 0.8341 (tp30) cc_final: 0.8089 (tp30) REVERT: A 776 LYS cc_start: 0.8834 (tppp) cc_final: 0.8359 (ttpt) REVERT: A 796 ASP cc_start: 0.8400 (t0) cc_final: 0.8144 (t0) REVERT: A 904 TYR cc_start: 0.8199 (m-10) cc_final: 0.7850 (m-80) REVERT: A 907 ASN cc_start: 0.9073 (t0) cc_final: 0.8782 (t0) REVERT: A 994 ASP cc_start: 0.8520 (t70) cc_final: 0.7935 (t0) REVERT: A 1102 TRP cc_start: 0.8904 (m100) cc_final: 0.8463 (m100) REVERT: B 18 LEU cc_start: 0.7445 (mm) cc_final: 0.6860 (tp) REVERT: B 137 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7438 (t0) REVERT: B 191 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7716 (mp0) REVERT: B 224 GLU cc_start: 0.7963 (mp0) cc_final: 0.7750 (mp0) REVERT: B 278 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8397 (ttpt) REVERT: B 353 TRP cc_start: 0.6959 (p-90) cc_final: 0.6737 (p-90) REVERT: B 408 ARG cc_start: 0.8223 (ppt170) cc_final: 0.7619 (ppt170) REVERT: B 414 GLN cc_start: 0.6503 (tp-100) cc_final: 0.5575 (tp-100) REVERT: B 453 TYR cc_start: 0.7734 (p90) cc_final: 0.7138 (p90) REVERT: B 565 PHE cc_start: 0.7278 (m-80) cc_final: 0.7004 (m-80) REVERT: B 586 ASP cc_start: 0.7841 (m-30) cc_final: 0.7392 (m-30) REVERT: B 619 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8057 (mp0) REVERT: B 644 GLN cc_start: 0.8527 (tp40) cc_final: 0.8319 (tp40) REVERT: B 773 GLU cc_start: 0.8222 (tp30) cc_final: 0.7960 (tp30) REVERT: B 825 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8277 (ttmm) REVERT: B 907 ASN cc_start: 0.9137 (t0) cc_final: 0.8904 (t0) REVERT: B 957 GLN cc_start: 0.8038 (tm130) cc_final: 0.7744 (tm-30) REVERT: B 979 ASP cc_start: 0.8298 (t0) cc_final: 0.8011 (t0) REVERT: C 177 MET cc_start: 0.3843 (ppp) cc_final: 0.3009 (ppp) REVERT: C 188 ASN cc_start: 0.7098 (t0) cc_final: 0.6403 (t0) REVERT: C 190 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7209 (mmm-85) REVERT: C 207 HIS cc_start: 0.7461 (t-90) cc_final: 0.7120 (t-90) REVERT: C 224 GLU cc_start: 0.8052 (mp0) cc_final: 0.7731 (mp0) REVERT: C 319 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8081 (mtp-110) REVERT: C 409 GLN cc_start: 0.8152 (mt0) cc_final: 0.7578 (mp10) REVERT: C 429 PHE cc_start: 0.8703 (t80) cc_final: 0.8493 (t80) REVERT: C 564 GLN cc_start: 0.7512 (tm-30) cc_final: 0.6921 (tm-30) REVERT: C 568 ASP cc_start: 0.7850 (t70) cc_final: 0.7497 (p0) REVERT: C 586 ASP cc_start: 0.8020 (m-30) cc_final: 0.7633 (m-30) REVERT: C 654 GLU cc_start: 0.8394 (pt0) cc_final: 0.8104 (pt0) REVERT: C 808 ASP cc_start: 0.7827 (t0) cc_final: 0.7287 (t0) REVERT: C 936 ASP cc_start: 0.8207 (m-30) cc_final: 0.7897 (m-30) REVERT: C 990 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8176 (mm-30) outliers start: 95 outliers final: 72 residues processed: 617 average time/residue: 0.1731 time to fit residues: 167.3612 Evaluate side-chains 616 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 539 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 47 optimal weight: 0.0170 chunk 163 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 245 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082532 restraints weight = 64588.747| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.17 r_work: 0.3172 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27336 Z= 0.155 Angle : 0.756 15.306 37350 Z= 0.356 Chirality : 0.047 0.523 4458 Planarity : 0.004 0.079 4650 Dihedral : 8.088 104.380 5510 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.01 % Allowed : 17.89 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3189 helix: 1.73 (0.20), residues: 714 sheet: -0.15 (0.18), residues: 699 loop : -0.90 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 765 TYR 0.022 0.001 TYR C1067 PHE 0.027 0.001 PHE C 133 TRP 0.014 0.001 TRP C 152 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00353 (27204) covalent geometry : angle 0.69762 (36996) SS BOND : bond 0.00585 ( 42) SS BOND : angle 2.33505 ( 84) hydrogen bonds : bond 0.03789 ( 1092) hydrogen bonds : angle 5.86770 ( 3054) link_ALPHA1-4 : bond 0.01565 ( 6) link_ALPHA1-4 : angle 2.71523 ( 18) link_BETA1-4 : bond 0.00423 ( 33) link_BETA1-4 : angle 1.55974 ( 99) link_BETA1-6 : bond 0.01446 ( 3) link_BETA1-6 : angle 1.77390 ( 9) link_NAG-ASN : bond 0.00535 ( 48) link_NAG-ASN : angle 4.15398 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 567 time to evaluate : 0.783 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: A 140 PHE cc_start: 0.8567 (p90) cc_final: 0.8327 (p90) REVERT: A 190 ARG cc_start: 0.8017 (mpt-90) cc_final: 0.7612 (mpt-90) REVERT: A 191 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: A 224 GLU cc_start: 0.8155 (mp0) cc_final: 0.7909 (mp0) REVERT: A 237 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.8173 (ttp80) REVERT: A 278 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8463 (ttmt) REVERT: A 324 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 392 PHE cc_start: 0.8484 (m-80) cc_final: 0.8047 (m-80) REVERT: A 429 PHE cc_start: 0.8497 (t80) cc_final: 0.8154 (t80) REVERT: A 534 VAL cc_start: 0.9350 (p) cc_final: 0.9075 (m) REVERT: A 563 GLN cc_start: 0.7739 (mt0) cc_final: 0.7399 (mt0) REVERT: A 586 ASP cc_start: 0.7970 (m-30) cc_final: 0.7495 (m-30) REVERT: A 599 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 675 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7138 (mt0) REVERT: A 773 GLU cc_start: 0.8282 (tp30) cc_final: 0.8042 (tp30) REVERT: A 776 LYS cc_start: 0.8809 (tppp) cc_final: 0.8334 (ttpt) REVERT: A 796 ASP cc_start: 0.8362 (t0) cc_final: 0.8114 (t0) REVERT: A 808 ASP cc_start: 0.7782 (t0) cc_final: 0.7574 (t0) REVERT: A 904 TYR cc_start: 0.8160 (m-10) cc_final: 0.7822 (m-80) REVERT: A 907 ASN cc_start: 0.9022 (t0) cc_final: 0.8744 (t0) REVERT: A 912 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 994 ASP cc_start: 0.8494 (t70) cc_final: 0.7899 (t0) REVERT: A 1102 TRP cc_start: 0.8877 (m100) cc_final: 0.8510 (m100) REVERT: B 18 LEU cc_start: 0.7378 (mm) cc_final: 0.6847 (tp) REVERT: B 137 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7412 (t0) REVERT: B 191 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7747 (mp0) REVERT: B 224 GLU cc_start: 0.7845 (mp0) cc_final: 0.7630 (mp0) REVERT: B 278 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8387 (ttpt) REVERT: B 408 ARG cc_start: 0.8187 (ppt170) cc_final: 0.7611 (ppt170) REVERT: B 414 GLN cc_start: 0.6460 (tp-100) cc_final: 0.5638 (tp-100) REVERT: B 442 ASP cc_start: 0.7206 (p0) cc_final: 0.6861 (p0) REVERT: B 564 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7129 (pp30) REVERT: B 565 PHE cc_start: 0.7245 (m-80) cc_final: 0.6885 (m-80) REVERT: B 586 ASP cc_start: 0.7833 (m-30) cc_final: 0.7386 (m-30) REVERT: B 619 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8007 (mp0) REVERT: B 644 GLN cc_start: 0.8553 (tp40) cc_final: 0.8351 (tp40) REVERT: B 773 GLU cc_start: 0.8226 (tp30) cc_final: 0.7981 (tp30) REVERT: B 780 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 825 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8308 (ttmm) REVERT: B 907 ASN cc_start: 0.9107 (t0) cc_final: 0.8869 (t0) REVERT: B 916 LEU cc_start: 0.8851 (tp) cc_final: 0.8643 (tp) REVERT: B 957 GLN cc_start: 0.7988 (tm130) cc_final: 0.7679 (tm-30) REVERT: B 979 ASP cc_start: 0.8285 (t0) cc_final: 0.7997 (t0) REVERT: C 177 MET cc_start: 0.3761 (ppp) cc_final: 0.2943 (ppp) REVERT: C 188 ASN cc_start: 0.7060 (t0) cc_final: 0.6308 (t0) REVERT: C 190 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: C 200 TYR cc_start: 0.6621 (t80) cc_final: 0.6282 (t80) REVERT: C 207 HIS cc_start: 0.7487 (t-90) cc_final: 0.7121 (t-90) REVERT: C 224 GLU cc_start: 0.7995 (mp0) cc_final: 0.7697 (mp0) REVERT: C 319 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.8095 (mtp-110) REVERT: C 408 ARG cc_start: 0.8512 (ppt170) cc_final: 0.8068 (ppt170) REVERT: C 409 GLN cc_start: 0.8178 (mt0) cc_final: 0.7768 (mt0) REVERT: C 429 PHE cc_start: 0.8680 (t80) cc_final: 0.8455 (t80) REVERT: C 442 ASP cc_start: 0.7609 (p0) cc_final: 0.7337 (p0) REVERT: C 564 GLN cc_start: 0.7515 (tm-30) cc_final: 0.6934 (tm-30) REVERT: C 568 ASP cc_start: 0.7835 (t70) cc_final: 0.7538 (p0) REVERT: C 654 GLU cc_start: 0.8370 (pt0) cc_final: 0.8079 (pt0) REVERT: C 808 ASP cc_start: 0.7788 (t0) cc_final: 0.7278 (t0) REVERT: C 912 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 936 ASP cc_start: 0.8174 (m-30) cc_final: 0.7853 (m-30) REVERT: C 990 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8193 (mm-30) REVERT: C 1004 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 1102 TRP cc_start: 0.8995 (m100) cc_final: 0.8589 (m100) outliers start: 85 outliers final: 63 residues processed: 606 average time/residue: 0.1751 time to fit residues: 166.4902 Evaluate side-chains 615 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 543 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 314 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 149 ASN C 388 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.100909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082697 restraints weight = 64588.628| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.19 r_work: 0.3170 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27336 Z= 0.152 Angle : 0.754 15.678 37350 Z= 0.355 Chirality : 0.047 0.504 4458 Planarity : 0.004 0.072 4650 Dihedral : 7.798 103.312 5510 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.87 % Allowed : 18.21 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3189 helix: 1.93 (0.20), residues: 687 sheet: -0.09 (0.19), residues: 690 loop : -0.84 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 237 TYR 0.021 0.001 TYR C1067 PHE 0.027 0.001 PHE A 157 TRP 0.020 0.001 TRP B 353 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00345 (27204) covalent geometry : angle 0.69730 (36996) SS BOND : bond 0.00466 ( 42) SS BOND : angle 2.25030 ( 84) hydrogen bonds : bond 0.03723 ( 1092) hydrogen bonds : angle 5.82693 ( 3054) link_ALPHA1-4 : bond 0.01598 ( 6) link_ALPHA1-4 : angle 2.80928 ( 18) link_BETA1-4 : bond 0.00393 ( 33) link_BETA1-4 : angle 1.57015 ( 99) link_BETA1-6 : bond 0.01440 ( 3) link_BETA1-6 : angle 1.78912 ( 9) link_NAG-ASN : bond 0.00519 ( 48) link_NAG-ASN : angle 4.07691 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 570 time to evaluate : 0.995 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: A 140 PHE cc_start: 0.8577 (p90) cc_final: 0.8367 (p90) REVERT: A 190 ARG cc_start: 0.8017 (mpt-90) cc_final: 0.7590 (mpt-90) REVERT: A 191 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7187 (mm-30) REVERT: A 202 LYS cc_start: 0.9017 (mptt) cc_final: 0.8752 (mppt) REVERT: A 224 GLU cc_start: 0.8194 (mp0) cc_final: 0.7921 (mp0) REVERT: A 237 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.8178 (ttp80) REVERT: A 278 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8459 (ttmt) REVERT: A 319 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8243 (mtp85) REVERT: A 324 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: A 355 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7588 (tpp80) REVERT: A 392 PHE cc_start: 0.8639 (m-80) cc_final: 0.8121 (m-80) REVERT: A 429 PHE cc_start: 0.8491 (t80) cc_final: 0.8123 (t80) REVERT: A 534 VAL cc_start: 0.9340 (p) cc_final: 0.9075 (m) REVERT: A 562 PHE cc_start: 0.7791 (p90) cc_final: 0.7541 (p90) REVERT: A 563 GLN cc_start: 0.7733 (mt0) cc_final: 0.7368 (mt0) REVERT: A 586 ASP cc_start: 0.7964 (m-30) cc_final: 0.7509 (m-30) REVERT: A 599 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 646 ARG cc_start: 0.8551 (mmt180) cc_final: 0.8339 (mmt180) REVERT: A 675 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7136 (mt0) REVERT: A 697 MET cc_start: 0.8275 (ptp) cc_final: 0.8075 (ptp) REVERT: A 773 GLU cc_start: 0.8273 (tp30) cc_final: 0.8043 (tp30) REVERT: A 776 LYS cc_start: 0.8792 (tppp) cc_final: 0.8326 (ttpt) REVERT: A 796 ASP cc_start: 0.8382 (t0) cc_final: 0.8137 (t0) REVERT: A 904 TYR cc_start: 0.8176 (m-10) cc_final: 0.7850 (m-80) REVERT: A 907 ASN cc_start: 0.9036 (t0) cc_final: 0.8759 (t0) REVERT: A 912 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8616 (p) REVERT: A 994 ASP cc_start: 0.8480 (t70) cc_final: 0.7879 (t0) REVERT: A 1102 TRP cc_start: 0.8864 (m100) cc_final: 0.8499 (m100) REVERT: B 18 LEU cc_start: 0.7473 (mm) cc_final: 0.6976 (tp) REVERT: B 191 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7743 (mp0) REVERT: B 224 GLU cc_start: 0.7687 (mp0) cc_final: 0.7485 (mp0) REVERT: B 278 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8346 (ttpt) REVERT: B 353 TRP cc_start: 0.6799 (p-90) cc_final: 0.6562 (p-90) REVERT: B 360 ASN cc_start: 0.8607 (t0) cc_final: 0.8279 (t0) REVERT: B 378 LYS cc_start: 0.7695 (mppt) cc_final: 0.7454 (mtmt) REVERT: B 408 ARG cc_start: 0.8192 (ppt170) cc_final: 0.7611 (ppt170) REVERT: B 414 GLN cc_start: 0.6481 (tp-100) cc_final: 0.5740 (tp-100) REVERT: B 564 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7042 (pp30) REVERT: B 565 PHE cc_start: 0.7238 (m-80) cc_final: 0.6684 (m-80) REVERT: B 586 ASP cc_start: 0.7854 (m-30) cc_final: 0.7387 (m-30) REVERT: B 619 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8049 (mp0) REVERT: B 644 GLN cc_start: 0.8578 (tp40) cc_final: 0.8377 (tp40) REVERT: B 773 GLU cc_start: 0.8224 (tp30) cc_final: 0.7978 (tp30) REVERT: B 780 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 825 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8309 (ttmm) REVERT: B 907 ASN cc_start: 0.9111 (t0) cc_final: 0.8874 (t0) REVERT: B 957 GLN cc_start: 0.8016 (tm130) cc_final: 0.7689 (tm-30) REVERT: B 979 ASP cc_start: 0.8248 (t0) cc_final: 0.7958 (t0) REVERT: C 153 MET cc_start: 0.8063 (pmm) cc_final: 0.7774 (pmm) REVERT: C 188 ASN cc_start: 0.7062 (t0) cc_final: 0.6310 (t0) REVERT: C 190 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7255 (mmm-85) REVERT: C 200 TYR cc_start: 0.6776 (t80) cc_final: 0.6508 (t80) REVERT: C 207 HIS cc_start: 0.7510 (t-90) cc_final: 0.7132 (t-90) REVERT: C 278 LYS cc_start: 0.8614 (tttm) cc_final: 0.8389 (tttt) REVERT: C 319 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8083 (mtp-110) REVERT: C 408 ARG cc_start: 0.8513 (ppt170) cc_final: 0.8077 (ppt170) REVERT: C 409 GLN cc_start: 0.8204 (mt0) cc_final: 0.7759 (mt0) REVERT: C 442 ASP cc_start: 0.7612 (p0) cc_final: 0.7340 (p0) REVERT: C 564 GLN cc_start: 0.7540 (tm-30) cc_final: 0.6965 (tm-30) REVERT: C 568 ASP cc_start: 0.7862 (t70) cc_final: 0.7559 (p0) REVERT: C 586 ASP cc_start: 0.8013 (m-30) cc_final: 0.7680 (m-30) REVERT: C 654 GLU cc_start: 0.8372 (pt0) cc_final: 0.8086 (pt0) REVERT: C 808 ASP cc_start: 0.7787 (t0) cc_final: 0.7266 (t0) REVERT: C 912 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8603 (p) REVERT: C 936 ASP cc_start: 0.8173 (m-30) cc_final: 0.7860 (m-30) REVERT: C 990 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8192 (mm-30) REVERT: C 1102 TRP cc_start: 0.8989 (m100) cc_final: 0.8590 (m100) outliers start: 81 outliers final: 61 residues processed: 611 average time/residue: 0.1883 time to fit residues: 178.3641 Evaluate side-chains 612 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 544 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 253 optimal weight: 0.0970 chunk 319 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 314 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 271 GLN C 388 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.101360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083159 restraints weight = 64689.427| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.17 r_work: 0.3180 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27336 Z= 0.145 Angle : 0.763 15.841 37350 Z= 0.359 Chirality : 0.047 0.492 4458 Planarity : 0.004 0.077 4650 Dihedral : 7.642 102.439 5510 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.66 % Allowed : 18.95 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3189 helix: 1.87 (0.20), residues: 708 sheet: -0.03 (0.19), residues: 681 loop : -0.85 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 237 TYR 0.021 0.001 TYR C1067 PHE 0.027 0.001 PHE A 157 TRP 0.012 0.001 TRP B 104 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00331 (27204) covalent geometry : angle 0.70803 (36996) SS BOND : bond 0.00461 ( 42) SS BOND : angle 2.21862 ( 84) hydrogen bonds : bond 0.03671 ( 1092) hydrogen bonds : angle 5.82427 ( 3054) link_ALPHA1-4 : bond 0.01583 ( 6) link_ALPHA1-4 : angle 2.75247 ( 18) link_BETA1-4 : bond 0.00417 ( 33) link_BETA1-4 : angle 1.54696 ( 99) link_BETA1-6 : bond 0.01372 ( 3) link_BETA1-6 : angle 1.81400 ( 9) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 4.05405 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 564 time to evaluate : 0.984 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: A 140 PHE cc_start: 0.8578 (p90) cc_final: 0.8371 (p90) REVERT: A 190 ARG cc_start: 0.8013 (mpt-90) cc_final: 0.7578 (mpt-90) REVERT: A 191 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: A 202 LYS cc_start: 0.9001 (mptt) cc_final: 0.8683 (mptt) REVERT: A 224 GLU cc_start: 0.8222 (mp0) cc_final: 0.7946 (mp0) REVERT: A 278 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8460 (ttmt) REVERT: A 319 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.8204 (mtp85) REVERT: A 324 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: A 346 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7609 (ttp-110) REVERT: A 347 PHE cc_start: 0.7302 (m-80) cc_final: 0.6998 (m-80) REVERT: A 355 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7423 (tpp80) REVERT: A 374 PHE cc_start: 0.8002 (m-80) cc_final: 0.7765 (m-80) REVERT: A 534 VAL cc_start: 0.9343 (p) cc_final: 0.9071 (m) REVERT: A 555 SER cc_start: 0.7481 (t) cc_final: 0.7280 (t) REVERT: A 562 PHE cc_start: 0.7840 (p90) cc_final: 0.7607 (p90) REVERT: A 563 GLN cc_start: 0.7713 (mt0) cc_final: 0.7341 (mt0) REVERT: A 599 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8775 (p) REVERT: A 646 ARG cc_start: 0.8538 (mmt180) cc_final: 0.8324 (mmt180) REVERT: A 675 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7119 (mt0) REVERT: A 773 GLU cc_start: 0.8263 (tp30) cc_final: 0.8038 (tp30) REVERT: A 776 LYS cc_start: 0.8782 (tppp) cc_final: 0.8324 (ttpt) REVERT: A 796 ASP cc_start: 0.8383 (t0) cc_final: 0.8122 (t0) REVERT: A 808 ASP cc_start: 0.7799 (t0) cc_final: 0.7472 (t0) REVERT: A 904 TYR cc_start: 0.8162 (m-10) cc_final: 0.7818 (m-80) REVERT: A 907 ASN cc_start: 0.9033 (t0) cc_final: 0.8757 (t0) REVERT: A 912 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8621 (p) REVERT: A 994 ASP cc_start: 0.8477 (t70) cc_final: 0.7892 (t0) REVERT: A 1102 TRP cc_start: 0.8842 (m100) cc_final: 0.8465 (m100) REVERT: B 18 LEU cc_start: 0.7503 (mm) cc_final: 0.7016 (tp) REVERT: B 191 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7747 (mp0) REVERT: B 278 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8211 (ttpt) REVERT: B 353 TRP cc_start: 0.6844 (p-90) cc_final: 0.6556 (p-90) REVERT: B 360 ASN cc_start: 0.8619 (t0) cc_final: 0.8300 (t0) REVERT: B 408 ARG cc_start: 0.8172 (ppt170) cc_final: 0.7536 (ppt170) REVERT: B 414 GLN cc_start: 0.6540 (tp-100) cc_final: 0.5789 (tp-100) REVERT: B 442 ASP cc_start: 0.7229 (p0) cc_final: 0.6874 (p0) REVERT: B 586 ASP cc_start: 0.7846 (m-30) cc_final: 0.7367 (m-30) REVERT: B 619 GLU cc_start: 0.8218 (mm-30) cc_final: 0.8007 (mp0) REVERT: B 773 GLU cc_start: 0.8217 (tp30) cc_final: 0.7967 (tp30) REVERT: B 780 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 808 ASP cc_start: 0.7773 (t0) cc_final: 0.7475 (t0) REVERT: B 825 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8328 (ttmm) REVERT: B 907 ASN cc_start: 0.9105 (t0) cc_final: 0.8865 (t0) REVERT: B 957 GLN cc_start: 0.8003 (tm130) cc_final: 0.7670 (tm-30) REVERT: B 979 ASP cc_start: 0.8251 (t0) cc_final: 0.7961 (t0) REVERT: C 34 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8079 (ttm-80) REVERT: C 153 MET cc_start: 0.8076 (pmm) cc_final: 0.7791 (pmm) REVERT: C 188 ASN cc_start: 0.7094 (t0) cc_final: 0.6368 (t0) REVERT: C 190 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7300 (mmm-85) REVERT: C 207 HIS cc_start: 0.7524 (t-90) cc_final: 0.7249 (t-90) REVERT: C 239 GLN cc_start: 0.8024 (mm110) cc_final: 0.7465 (mm110) REVERT: C 278 LYS cc_start: 0.8617 (tttm) cc_final: 0.8357 (tttt) REVERT: C 319 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.8052 (mtp-110) REVERT: C 408 ARG cc_start: 0.8516 (ppt170) cc_final: 0.8218 (ppt170) REVERT: C 409 GLN cc_start: 0.8157 (mt0) cc_final: 0.7664 (mt0) REVERT: C 442 ASP cc_start: 0.7594 (p0) cc_final: 0.7321 (p0) REVERT: C 457 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6448 (tpt170) REVERT: C 564 GLN cc_start: 0.7558 (tm-30) cc_final: 0.6973 (tm-30) REVERT: C 568 ASP cc_start: 0.7821 (t70) cc_final: 0.7546 (p0) REVERT: C 586 ASP cc_start: 0.8006 (m-30) cc_final: 0.7651 (m-30) REVERT: C 654 GLU cc_start: 0.8378 (pt0) cc_final: 0.8100 (pt0) REVERT: C 808 ASP cc_start: 0.7790 (t0) cc_final: 0.7269 (t0) REVERT: C 904 TYR cc_start: 0.8060 (m-80) cc_final: 0.7851 (m-10) REVERT: C 912 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 936 ASP cc_start: 0.8172 (m-30) cc_final: 0.7858 (m-30) REVERT: C 990 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 1004 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8487 (tt) REVERT: C 1102 TRP cc_start: 0.8975 (m100) cc_final: 0.8587 (m100) outliers start: 75 outliers final: 60 residues processed: 606 average time/residue: 0.1859 time to fit residues: 175.7409 Evaluate side-chains 625 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 555 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 157 optimal weight: 3.9990 chunk 277 optimal weight: 0.1980 chunk 275 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 133 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 149 ASN C 388 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.101747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083536 restraints weight = 64291.585| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.18 r_work: 0.3192 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 27336 Z= 0.140 Angle : 0.760 15.912 37350 Z= 0.358 Chirality : 0.047 0.480 4458 Planarity : 0.004 0.066 4650 Dihedral : 7.466 101.440 5510 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.55 % Allowed : 19.41 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3189 helix: 1.92 (0.20), residues: 708 sheet: -0.01 (0.19), residues: 684 loop : -0.84 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 237 TYR 0.021 0.001 TYR C1067 PHE 0.024 0.001 PHE C 392 TRP 0.011 0.001 TRP B 104 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00324 (27204) covalent geometry : angle 0.70720 (36996) SS BOND : bond 0.00435 ( 42) SS BOND : angle 2.16792 ( 84) hydrogen bonds : bond 0.03632 ( 1092) hydrogen bonds : angle 5.82780 ( 3054) link_ALPHA1-4 : bond 0.01570 ( 6) link_ALPHA1-4 : angle 2.77309 ( 18) link_BETA1-4 : bond 0.00419 ( 33) link_BETA1-4 : angle 1.52966 ( 99) link_BETA1-6 : bond 0.01403 ( 3) link_BETA1-6 : angle 1.81699 ( 9) link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 3.95242 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6801.12 seconds wall clock time: 117 minutes 22.79 seconds (7042.79 seconds total)