Starting phenix.real_space_refine on Fri Mar 6 01:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vv5_21391/03_2026/6vv5_21391.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vv5_21391/03_2026/6vv5_21391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vv5_21391/03_2026/6vv5_21391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vv5_21391/03_2026/6vv5_21391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vv5_21391/03_2026/6vv5_21391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vv5_21391/03_2026/6vv5_21391.map" } resolution = 3.5 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 17100 2.51 5 N 4212 2.21 5 O 5415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26838 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "B" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "C" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.41, per 1000 atoms: 0.24 Number of scatterers: 26838 At special positions: 0 Unit cell: (141.45, 133.4, 171.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5415 8.00 N 4212 7.00 C 17100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.04 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.07 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.06 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.09 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.10 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.02 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.04 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.07 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.06 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.09 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.10 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.02 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.07 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.09 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.10 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.02 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA N 3 " - " MAN N 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " MAN D 6 " - " MAN D 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " BETA1-2 " MAN D 6 " - " NAG D 7 " " MAN N 6 " - " NAG N 7 " " MAN X 6 " - " NAG X 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " 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 X 2 " - " BMA X 3 " " 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 b 2 " - " BMA b 3 " " 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-ASN " NAG A1401 " - " ASN A 216 " " NAG A1402 " - " ASN A 300 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 781 " " NAG A1405 " - " ASN A1249 " " NAG B1401 " - " ASN B 216 " " NAG B1402 " - " ASN B 300 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 781 " " NAG B1405 " - " ASN B1249 " " NAG C1401 " - " ASN C 216 " " NAG C1402 " - " ASN C 300 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 781 " " NAG C1405 " - " ASN C1249 " " NAG D 1 " - " ASN A 264 " " NAG E 1 " - " ASN A 344 " " NAG F 1 " - " ASN A 514 " " NAG G 1 " - " ASN A 556 " " NAG H 1 " - " ASN A 688 " " NAG I 1 " - " ASN A 726 " " NAG J 1 " - " ASN A 743 " " NAG K 1 " - " ASN A 787 " " NAG L 1 " - " ASN A 873 " " NAG M 1 " - " ASN A1232 " " NAG N 1 " - " ASN B 264 " " NAG O 1 " - " ASN B 344 " " NAG P 1 " - " ASN B 514 " " NAG Q 1 " - " ASN B 556 " " NAG R 1 " - " ASN B 688 " " NAG S 1 " - " ASN B 726 " " NAG T 1 " - " ASN B 743 " " NAG U 1 " - " ASN B 787 " " NAG V 1 " - " ASN B 873 " " NAG W 1 " - " ASN B1232 " " NAG X 1 " - " ASN C 264 " " NAG Y 1 " - " ASN C 344 " " NAG Z 1 " - " ASN C 514 " " NAG a 1 " - " ASN C 556 " " NAG b 1 " - " ASN C 688 " " NAG c 1 " - " ASN C 726 " " NAG d 1 " - " ASN C 743 " " NAG e 1 " - " ASN C 787 " " NAG f 1 " - " ASN C 873 " " NAG g 1 " - " ASN C1232 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 24.0% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 826 through 852 Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 993 through 1014 removed outlier: 3.936A pdb=" N GLN A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1020 Processing helix chain 'A' and resid 1030 through 1044 Processing helix chain 'A' and resid 1048 through 1055 Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1072 Processing helix chain 'A' and resid 1075 through 1123 Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1241 Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 826 through 852 Processing helix chain 'B' and resid 855 through 860 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 960 Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 973 through 986 Processing helix chain 'B' and resid 993 through 1014 removed outlier: 3.936A pdb=" N GLN B 997 " --> pdb=" O GLN B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1020 Processing helix chain 'B' and resid 1030 through 1044 Processing helix chain 'B' and resid 1048 through 1055 Processing helix chain 'B' and resid 1056 through 1058 No H-bonds generated for 'chain 'B' and resid 1056 through 1058' Processing helix chain 'B' and resid 1066 through 1072 Processing helix chain 'B' and resid 1075 through 1123 Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1237 through 1241 Processing helix chain 'B' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 826 through 852 Processing helix chain 'C' and resid 855 through 860 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 946 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 973 through 986 Processing helix chain 'C' and resid 993 through 1014 removed outlier: 3.936A pdb=" N GLN C 997 " --> pdb=" O GLN C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1020 Processing helix chain 'C' and resid 1030 through 1044 Processing helix chain 'C' and resid 1048 through 1055 Processing helix chain 'C' and resid 1056 through 1058 No H-bonds generated for 'chain 'C' and resid 1056 through 1058' Processing helix chain 'C' and resid 1066 through 1072 Processing helix chain 'C' and resid 1075 through 1123 Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1241 Processing helix chain 'C' and resid 1247 through 1254 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 154 removed outlier: 3.524A pdb=" N ARG A 191 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 322 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 441 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 320 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A 443 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 318 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 452 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.989A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 5.284A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU A 627 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N LEU A 583 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS A 614 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 605 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 786 Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 798 removed outlier: 7.157A pdb=" N GLY A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA A1146 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A1152 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A1144 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A1154 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A1142 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR A1156 " --> pdb=" O ILE A1140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 3.520A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 180 through 184 Processing sheet with id=AC1, first strand: chain 'B' and resid 148 through 154 removed outlier: 3.524A pdb=" N ARG B 191 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 322 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 441 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG B 320 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER B 443 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 318 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 452 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG B 460 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 296 through 298 removed outlier: 6.990A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 502 removed outlier: 5.284A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER B 511 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER B 552 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 513 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE B 554 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 515 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN B 556 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 517 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR B 558 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 519 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY B 625 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU B 627 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N LEU B 583 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER B 511 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER B 552 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 513 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE B 554 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 515 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN B 556 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 517 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR B 558 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 519 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS B 614 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY B 605 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 780 through 786 Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 798 removed outlier: 7.157A pdb=" N GLY B1150 " --> pdb=" O ALA B1146 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA B1146 " --> pdb=" O GLY B1150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B1152 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B1144 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1154 " --> pdb=" O SER B1142 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B1142 " --> pdb=" O LEU B1154 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR B1156 " --> pdb=" O ILE B1140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD4, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.520A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 51 Processing sheet with id=AD7, first strand: chain 'C' and resid 180 through 184 Processing sheet with id=AD8, first strand: chain 'C' and resid 148 through 154 removed outlier: 3.524A pdb=" N ARG C 191 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN C 322 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 441 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 320 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER C 443 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA C 318 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU C 452 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG C 460 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.989A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 709 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 499 through 502 removed outlier: 5.283A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 531 through 536 removed outlier: 6.833A pdb=" N SER C 511 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER C 552 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 513 " --> pdb=" O SER C 552 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE C 554 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 515 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASN C 556 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 517 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 558 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 519 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C 625 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU C 627 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N LEU C 583 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 531 through 536 removed outlier: 6.833A pdb=" N SER C 511 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER C 552 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 513 " --> pdb=" O SER C 552 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE C 554 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 515 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASN C 556 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 517 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 558 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 519 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AE8, first strand: chain 'C' and resid 780 through 786 Processing sheet with id=AE9, first strand: chain 'C' and resid 789 through 798 removed outlier: 7.157A pdb=" N GLY C1150 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA C1146 " --> pdb=" O GLY C1150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C1152 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL C1144 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C1154 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER C1142 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C1156 " --> pdb=" O ILE C1140 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF2, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.520A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1187 through 1190 1129 hydrogen bonds defined for protein. 3063 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: 7.18 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5483 1.32 - 1.45: 8317 1.45 - 1.58: 13386 1.58 - 1.71: 12 1.71 - 1.84: 138 Bond restraints: 27336 Sorted by residual: bond pdb=" C10 PAM B1406 " pdb=" C9 PAM B1406 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C10 PAM C1406 " pdb=" C9 PAM C1406 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C10 PAM C1407 " pdb=" C9 PAM C1407 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" C10 PAM A1406 " pdb=" C9 PAM A1406 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" C10 PAM A1407 " pdb=" C9 PAM A1407 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.29e+01 ... (remaining 27331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 34197 2.90 - 5.79: 2651 5.79 - 8.69: 247 8.69 - 11.58: 9 11.58 - 14.48: 12 Bond angle restraints: 37116 Sorted by residual: angle pdb=" C CYS C 572 " pdb=" N PRO C 573 " pdb=" CA PRO C 573 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C CYS A 572 " pdb=" N PRO A 573 " pdb=" CA PRO A 573 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C CYS B 572 " pdb=" N PRO B 573 " pdb=" CA PRO B 573 " ideal model delta sigma weight residual 119.82 127.71 -7.89 9.80e-01 1.04e+00 6.48e+01 angle pdb=" C TYR A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta sigma weight residual 119.56 127.35 -7.79 1.01e+00 9.80e-01 5.94e+01 angle pdb=" C TYR C 606 " pdb=" N PRO C 607 " pdb=" CA PRO C 607 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.91e+01 ... (remaining 37111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 16773 21.77 - 43.54: 396 43.54 - 65.32: 162 65.32 - 87.09: 66 87.09 - 108.86: 27 Dihedral angle restraints: 17424 sinusoidal: 7848 harmonic: 9576 Sorted by residual: dihedral pdb=" CB CYS B1173 " pdb=" SG CYS B1173 " pdb=" SG CYS B1226 " pdb=" CB CYS B1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.35 49.35 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS C1173 " pdb=" SG CYS C1173 " pdb=" SG CYS C1226 " pdb=" CB CYS C1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.34 49.34 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS A1173 " pdb=" SG CYS A1173 " pdb=" SG CYS A1226 " pdb=" CB CYS A1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.33 49.33 1 1.00e+01 1.00e-02 3.34e+01 ... (remaining 17421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3180 0.088 - 0.176: 1185 0.176 - 0.263: 231 0.263 - 0.351: 21 0.351 - 0.439: 3 Chirality restraints: 4620 Sorted by residual: chirality pdb=" C1 NAG D 7 " pdb=" O2 MAN D 6 " pdb=" C2 NAG D 7 " pdb=" O5 NAG D 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG N 7 " pdb=" O2 MAN N 6 " pdb=" C2 NAG N 7 " pdb=" O5 NAG N 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 NAG X 7 " pdb=" O2 MAN X 6 " pdb=" C2 NAG X 7 " pdb=" O5 NAG X 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 4617 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG N 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG D 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG X 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.149 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6522 2.79 - 3.32: 24512 3.32 - 3.84: 44904 3.84 - 4.37: 53060 4.37 - 4.90: 88789 Nonbonded interactions: 217787 Sorted by model distance: nonbonded pdb=" O3 NAG b 1 " pdb=" O7 NAG b 1 " model vdw 2.262 3.040 nonbonded pdb=" O3 NAG R 1 " pdb=" O7 NAG R 1 " model vdw 2.263 3.040 nonbonded pdb=" O3 NAG H 1 " pdb=" O7 NAG H 1 " model vdw 2.263 3.040 nonbonded pdb=" O4 BMA X 3 " pdb=" O2 MAN X 8 " model vdw 2.296 3.040 nonbonded pdb=" O4 BMA D 3 " pdb=" O2 MAN D 8 " model vdw 2.297 3.040 ... (remaining 217782 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'b' } 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 group one per residue 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: 1.410 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.430 Find NCS groups from input model: 0.970 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.017 0.194 27474 Z= 0.940 Angle : 1.679 14.477 37488 Z= 1.104 Chirality : 0.089 0.439 4620 Planarity : 0.026 0.301 4584 Dihedral : 12.915 108.859 11112 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.30 % Rotamer: Outliers : 1.26 % Allowed : 1.26 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3177 helix: 0.72 (0.17), residues: 678 sheet: 1.53 (0.18), residues: 705 loop : 0.22 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1112 TYR 0.083 0.008 TYR A 676 PHE 0.036 0.005 PHE A 185 TRP 0.020 0.005 TRP C 439 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01741 (27336) covalent geometry : angle 1.67576 (37116) SS BOND : bond 0.02788 ( 42) SS BOND : angle 2.59710 ( 84) hydrogen bonds : bond 0.17105 ( 1099) hydrogen bonds : angle 7.67282 ( 3063) link_ALPHA1-2 : bond 0.00059 ( 3) link_ALPHA1-2 : angle 0.58301 ( 9) link_ALPHA1-3 : bond 0.00799 ( 3) link_ALPHA1-3 : angle 1.95184 ( 9) link_ALPHA1-6 : bond 0.00128 ( 6) link_ALPHA1-6 : angle 1.33015 ( 18) link_BETA1-2 : bond 0.00049 ( 3) link_BETA1-2 : angle 1.91459 ( 9) link_BETA1-4 : bond 0.00292 ( 36) link_BETA1-4 : angle 1.62131 ( 108) link_NAG-ASN : bond 0.00225 ( 45) link_NAG-ASN : angle 1.81841 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 598 time to evaluate : 0.888 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 206 TYR cc_start: 0.6123 (m-80) cc_final: 0.5643 (m-10) REVERT: A 263 SER cc_start: 0.9264 (t) cc_final: 0.9038 (p) REVERT: A 303 ILE cc_start: 0.9195 (pt) cc_final: 0.8951 (pt) REVERT: A 850 SER cc_start: 0.8970 (t) cc_final: 0.8704 (m) REVERT: A 899 ASP cc_start: 0.8453 (t70) cc_final: 0.8071 (t0) REVERT: A 1059 ASN cc_start: 0.8051 (t0) cc_final: 0.7843 (p0) REVERT: A 1104 LYS cc_start: 0.8805 (tptt) cc_final: 0.8574 (mtpt) REVERT: B 397 GLU cc_start: 0.8234 (tt0) cc_final: 0.7767 (tt0) REVERT: B 850 SER cc_start: 0.8968 (t) cc_final: 0.8689 (m) REVERT: B 899 ASP cc_start: 0.8526 (t70) cc_final: 0.8050 (t0) REVERT: B 1059 ASN cc_start: 0.8252 (t0) cc_final: 0.8042 (p0) REVERT: B 1104 LYS cc_start: 0.8626 (tptt) cc_final: 0.8302 (mtpt) REVERT: C 38 LYS cc_start: 0.8017 (mttm) cc_final: 0.7778 (mtpt) REVERT: C 303 ILE cc_start: 0.9223 (pt) cc_final: 0.8919 (pt) REVERT: C 758 LYS cc_start: 0.8244 (pttt) cc_final: 0.8031 (tptt) REVERT: C 850 SER cc_start: 0.8983 (t) cc_final: 0.8585 (m) REVERT: C 899 ASP cc_start: 0.8394 (t70) cc_final: 0.8084 (t0) REVERT: C 1059 ASN cc_start: 0.8085 (t0) cc_final: 0.7796 (p0) REVERT: C 1104 LYS cc_start: 0.8797 (tptt) cc_final: 0.8537 (mtpt) outliers start: 36 outliers final: 14 residues processed: 620 average time/residue: 0.1726 time to fit residues: 167.7854 Evaluate side-chains 276 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 714 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 356 HIS A 445 ASN A1045 GLN A1139 HIS B 282 ASN B 295 GLN B 445 ASN B1045 GLN B1051 GLN B1061 GLN B1139 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS C 282 ASN C 356 HIS C 445 ASN C 816 ASN C 821 GLN C 988 GLN C1045 GLN C1058 HIS C1139 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117346 restraints weight = 35730.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120260 restraints weight = 22384.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122163 restraints weight = 16672.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123364 restraints weight = 13839.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123971 restraints weight = 12306.531| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27474 Z= 0.163 Angle : 0.751 23.385 37488 Z= 0.363 Chirality : 0.051 0.556 4620 Planarity : 0.004 0.040 4584 Dihedral : 10.433 89.130 5563 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.36 % Allowed : 7.64 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3177 helix: 1.87 (0.19), residues: 714 sheet: 1.18 (0.18), residues: 729 loop : -0.17 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 924 TYR 0.017 0.002 TYR B 227 PHE 0.025 0.002 PHE A 39 TRP 0.010 0.002 TRP A 168 HIS 0.008 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00346 (27336) covalent geometry : angle 0.69649 (37116) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.34841 ( 84) hydrogen bonds : bond 0.05883 ( 1099) hydrogen bonds : angle 5.95300 ( 3063) link_ALPHA1-2 : bond 0.00653 ( 3) link_ALPHA1-2 : angle 1.75929 ( 9) link_ALPHA1-3 : bond 0.02058 ( 3) link_ALPHA1-3 : angle 1.51569 ( 9) link_ALPHA1-6 : bond 0.01579 ( 6) link_ALPHA1-6 : angle 2.23522 ( 18) link_BETA1-2 : bond 0.00211 ( 3) link_BETA1-2 : angle 2.45603 ( 9) link_BETA1-4 : bond 0.00624 ( 36) link_BETA1-4 : angle 1.70817 ( 108) link_NAG-ASN : bond 0.00638 ( 45) link_NAG-ASN : angle 4.29731 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: A 263 SER cc_start: 0.9122 (t) cc_final: 0.8819 (p) REVERT: A 850 SER cc_start: 0.8893 (t) cc_final: 0.8647 (m) REVERT: A 899 ASP cc_start: 0.8159 (t70) cc_final: 0.7662 (t0) REVERT: A 1051 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7464 (mt0) REVERT: A 1057 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7563 (tm-30) REVERT: A 1181 THR cc_start: 0.9136 (t) cc_final: 0.8858 (p) REVERT: B 397 GLU cc_start: 0.8358 (tt0) cc_final: 0.7755 (tt0) REVERT: B 850 SER cc_start: 0.9013 (t) cc_final: 0.8757 (m) REVERT: B 899 ASP cc_start: 0.8204 (t70) cc_final: 0.7680 (t0) REVERT: B 1051 GLN cc_start: 0.8018 (mm110) cc_final: 0.7535 (mt0) REVERT: C 38 LYS cc_start: 0.8082 (mttm) cc_final: 0.7700 (mtpt) REVERT: C 303 ILE cc_start: 0.9158 (pt) cc_final: 0.8932 (pt) REVERT: C 372 TYR cc_start: 0.7980 (m-10) cc_final: 0.7675 (m-80) REVERT: C 704 GLU cc_start: 0.7644 (pt0) cc_final: 0.7431 (pt0) REVERT: C 850 SER cc_start: 0.8826 (t) cc_final: 0.8596 (m) REVERT: C 899 ASP cc_start: 0.7993 (t70) cc_final: 0.7549 (t0) REVERT: C 1051 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7677 (mt0) outliers start: 39 outliers final: 31 residues processed: 352 average time/residue: 0.1577 time to fit residues: 92.1449 Evaluate side-chains 258 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 225 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 235 optimal weight: 0.2980 chunk 318 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS A 356 HIS A 571 ASN A 821 GLN A1059 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 571 ASN B1061 GLN C 147 ASN C 979 GLN C 996 GLN C1051 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103642 restraints weight = 37237.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106184 restraints weight = 24216.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107825 restraints weight = 18491.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108827 restraints weight = 15646.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109490 restraints weight = 14104.673| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 27474 Z= 0.278 Angle : 0.768 12.119 37488 Z= 0.375 Chirality : 0.050 0.259 4620 Planarity : 0.004 0.041 4584 Dihedral : 8.105 59.694 5548 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.48 % Allowed : 8.66 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3177 helix: 1.46 (0.19), residues: 720 sheet: 0.70 (0.18), residues: 747 loop : -0.66 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1090 TYR 0.025 0.002 TYR A 652 PHE 0.024 0.002 PHE B 39 TRP 0.009 0.002 TRP A 259 HIS 0.012 0.002 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00665 (27336) covalent geometry : angle 0.73041 (37116) SS BOND : bond 0.00578 ( 42) SS BOND : angle 1.61491 ( 84) hydrogen bonds : bond 0.05837 ( 1099) hydrogen bonds : angle 5.64118 ( 3063) link_ALPHA1-2 : bond 0.00415 ( 3) link_ALPHA1-2 : angle 1.59452 ( 9) link_ALPHA1-3 : bond 0.01286 ( 3) link_ALPHA1-3 : angle 2.00479 ( 9) link_ALPHA1-6 : bond 0.01854 ( 6) link_ALPHA1-6 : angle 3.13555 ( 18) link_BETA1-2 : bond 0.00655 ( 3) link_BETA1-2 : angle 3.51581 ( 9) link_BETA1-4 : bond 0.00441 ( 36) link_BETA1-4 : angle 1.69396 ( 108) link_NAG-ASN : bond 0.00757 ( 45) link_NAG-ASN : angle 3.27451 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 248 time to evaluate : 0.953 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 39 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 214 MET cc_start: 0.7793 (tmm) cc_final: 0.6866 (tmm) REVERT: A 899 ASP cc_start: 0.8280 (t70) cc_final: 0.7787 (t0) REVERT: A 1051 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7649 (mt0) REVERT: A 1057 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7628 (tm-30) REVERT: B 157 HIS cc_start: 0.3324 (t-90) cc_final: 0.3099 (t70) REVERT: B 899 ASP cc_start: 0.8278 (t70) cc_final: 0.7752 (t0) REVERT: B 984 TYR cc_start: 0.7753 (m-80) cc_final: 0.7305 (t80) REVERT: B 1051 GLN cc_start: 0.7931 (mm110) cc_final: 0.7447 (mt0) REVERT: C 38 LYS cc_start: 0.8162 (mttm) cc_final: 0.7707 (mtpt) REVERT: C 303 ILE cc_start: 0.9270 (pt) cc_final: 0.9053 (pt) REVERT: C 397 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: C 545 ASP cc_start: 0.7722 (m-30) cc_final: 0.7487 (t0) REVERT: C 899 ASP cc_start: 0.8160 (t70) cc_final: 0.7623 (t0) REVERT: C 1061 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8088 (mm-40) REVERT: C 1082 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7643 (mt0) outliers start: 71 outliers final: 51 residues processed: 305 average time/residue: 0.1546 time to fit residues: 78.0521 Evaluate side-chains 261 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 188 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 165 optimal weight: 0.4980 chunk 87 optimal weight: 0.4980 chunk 276 optimal weight: 0.0000 chunk 151 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS A 571 ASN A 979 GLN A 996 GLN A1029 ASN A1059 ASN A1061 GLN B 295 GLN B 356 HIS B 571 ASN B1029 ASN C1029 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112986 restraints weight = 35587.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115690 restraints weight = 22755.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117468 restraints weight = 17227.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118573 restraints weight = 14411.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119164 restraints weight = 12925.644| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27474 Z= 0.115 Angle : 0.562 8.516 37488 Z= 0.279 Chirality : 0.044 0.229 4620 Planarity : 0.003 0.042 4584 Dihedral : 6.856 59.052 5546 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.68 % Allowed : 10.61 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3177 helix: 2.01 (0.19), residues: 744 sheet: 0.72 (0.18), residues: 729 loop : -0.56 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1085 TYR 0.026 0.001 TYR B 407 PHE 0.014 0.001 PHE C 296 TRP 0.005 0.001 TRP A 168 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00237 (27336) covalent geometry : angle 0.52903 (37116) SS BOND : bond 0.00282 ( 42) SS BOND : angle 0.88596 ( 84) hydrogen bonds : bond 0.04500 ( 1099) hydrogen bonds : angle 5.22487 ( 3063) link_ALPHA1-2 : bond 0.00333 ( 3) link_ALPHA1-2 : angle 1.37709 ( 9) link_ALPHA1-3 : bond 0.01358 ( 3) link_ALPHA1-3 : angle 1.49836 ( 9) link_ALPHA1-6 : bond 0.01844 ( 6) link_ALPHA1-6 : angle 3.17876 ( 18) link_BETA1-2 : bond 0.00514 ( 3) link_BETA1-2 : angle 2.33558 ( 9) link_BETA1-4 : bond 0.00451 ( 36) link_BETA1-4 : angle 1.36849 ( 108) link_NAG-ASN : bond 0.00691 ( 45) link_NAG-ASN : angle 2.60850 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.907 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 214 MET cc_start: 0.8121 (tmm) cc_final: 0.7214 (tmm) REVERT: A 899 ASP cc_start: 0.8070 (t70) cc_final: 0.7668 (t0) REVERT: A 1051 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7408 (mt0) REVERT: A 1057 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 38 LYS cc_start: 0.8084 (mttm) cc_final: 0.7730 (mttm) REVERT: B 111 LYS cc_start: 0.6351 (pttp) cc_final: 0.5864 (tptt) REVERT: B 214 MET cc_start: 0.7491 (ttp) cc_final: 0.7073 (ttp) REVERT: B 899 ASP cc_start: 0.8063 (t70) cc_final: 0.7543 (t0) REVERT: B 984 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 1051 GLN cc_start: 0.7710 (mm110) cc_final: 0.7419 (mt0) REVERT: C 38 LYS cc_start: 0.8198 (mttm) cc_final: 0.7763 (mtpt) REVERT: C 899 ASP cc_start: 0.7892 (t70) cc_final: 0.7387 (t0) outliers start: 48 outliers final: 31 residues processed: 287 average time/residue: 0.1545 time to fit residues: 73.3764 Evaluate side-chains 252 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 1010 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 170 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 270 HIS A1058 HIS B 187 ASN B 295 GLN B1061 GLN C 571 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110569 restraints weight = 35811.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113131 restraints weight = 23080.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114830 restraints weight = 17577.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115833 restraints weight = 14794.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116555 restraints weight = 13279.616| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27474 Z= 0.208 Angle : 0.617 8.980 37488 Z= 0.307 Chirality : 0.045 0.199 4620 Planarity : 0.004 0.042 4584 Dihedral : 6.599 59.536 5542 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.20 % Allowed : 10.58 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3177 helix: 1.85 (0.19), residues: 744 sheet: 0.59 (0.18), residues: 747 loop : -0.70 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1090 TYR 0.015 0.002 TYR A 652 PHE 0.017 0.001 PHE C 39 TRP 0.006 0.001 TRP A 259 HIS 0.007 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00496 (27336) covalent geometry : angle 0.58654 (37116) SS BOND : bond 0.00599 ( 42) SS BOND : angle 1.19208 ( 84) hydrogen bonds : bond 0.04935 ( 1099) hydrogen bonds : angle 5.28875 ( 3063) link_ALPHA1-2 : bond 0.00301 ( 3) link_ALPHA1-2 : angle 1.34714 ( 9) link_ALPHA1-3 : bond 0.01362 ( 3) link_ALPHA1-3 : angle 1.37385 ( 9) link_ALPHA1-6 : bond 0.01497 ( 6) link_ALPHA1-6 : angle 2.90914 ( 18) link_BETA1-2 : bond 0.00031 ( 3) link_BETA1-2 : angle 3.08450 ( 9) link_BETA1-4 : bond 0.00474 ( 36) link_BETA1-4 : angle 1.33546 ( 108) link_NAG-ASN : bond 0.00565 ( 45) link_NAG-ASN : angle 2.59861 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8043 (mttp) cc_final: 0.7508 (mtpt) REVERT: A 214 MET cc_start: 0.8008 (tmm) cc_final: 0.6773 (tmm) REVERT: A 899 ASP cc_start: 0.8241 (t70) cc_final: 0.7798 (t0) REVERT: A 1051 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7441 (mt0) REVERT: A 1057 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 1124 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.8962 (mttm) REVERT: B 38 LYS cc_start: 0.8180 (mttm) cc_final: 0.7803 (mttm) REVERT: B 111 LYS cc_start: 0.6013 (pttp) cc_final: 0.5721 (pttm) REVERT: B 214 MET cc_start: 0.7490 (ttp) cc_final: 0.7017 (ttp) REVERT: B 899 ASP cc_start: 0.8217 (t70) cc_final: 0.7796 (t0) REVERT: B 984 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7233 (t80) REVERT: B 1051 GLN cc_start: 0.7718 (mm110) cc_final: 0.7474 (mt0) REVERT: C 38 LYS cc_start: 0.8111 (mttm) cc_final: 0.7688 (mtpt) REVERT: C 97 GLN cc_start: 0.7047 (mt0) cc_final: 0.6844 (mp10) REVERT: C 397 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: C 899 ASP cc_start: 0.8121 (t70) cc_final: 0.7707 (t0) REVERT: C 984 TYR cc_start: 0.7597 (m-80) cc_final: 0.7200 (t80) REVERT: C 1082 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7607 (mt0) outliers start: 63 outliers final: 47 residues processed: 286 average time/residue: 0.1558 time to fit residues: 73.2355 Evaluate side-chains 274 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 272 optimal weight: 0.5980 chunk 304 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113865 restraints weight = 35742.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116560 restraints weight = 22812.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118326 restraints weight = 17224.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119406 restraints weight = 14415.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120093 restraints weight = 12888.989| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27474 Z= 0.110 Angle : 0.533 9.489 37488 Z= 0.266 Chirality : 0.043 0.206 4620 Planarity : 0.003 0.042 4584 Dihedral : 6.206 59.694 5542 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.78 % Allowed : 11.38 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3177 helix: 2.12 (0.19), residues: 747 sheet: 0.63 (0.19), residues: 720 loop : -0.69 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1085 TYR 0.020 0.001 TYR C 407 PHE 0.014 0.001 PHE C 36 TRP 0.005 0.001 TRP C 189 HIS 0.002 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00235 (27336) covalent geometry : angle 0.50497 (37116) SS BOND : bond 0.00243 ( 42) SS BOND : angle 0.90750 ( 84) hydrogen bonds : bond 0.04182 ( 1099) hydrogen bonds : angle 5.04463 ( 3063) link_ALPHA1-2 : bond 0.00355 ( 3) link_ALPHA1-2 : angle 1.35292 ( 9) link_ALPHA1-3 : bond 0.01367 ( 3) link_ALPHA1-3 : angle 1.17781 ( 9) link_ALPHA1-6 : bond 0.01466 ( 6) link_ALPHA1-6 : angle 2.60018 ( 18) link_BETA1-2 : bond 0.00379 ( 3) link_BETA1-2 : angle 2.18824 ( 9) link_BETA1-4 : bond 0.00451 ( 36) link_BETA1-4 : angle 1.29482 ( 108) link_NAG-ASN : bond 0.00548 ( 45) link_NAG-ASN : angle 2.34063 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.791 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 214 MET cc_start: 0.7999 (tmm) cc_final: 0.6751 (tmm) REVERT: A 899 ASP cc_start: 0.8034 (t70) cc_final: 0.7824 (t70) REVERT: A 1051 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7361 (mt0) REVERT: A 1057 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 1124 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8912 (mttm) REVERT: B 214 MET cc_start: 0.7496 (ttp) cc_final: 0.6982 (ttp) REVERT: B 545 ASP cc_start: 0.7733 (m-30) cc_final: 0.7444 (t0) REVERT: B 899 ASP cc_start: 0.7955 (t70) cc_final: 0.7606 (t0) REVERT: B 984 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7153 (t80) REVERT: C 899 ASP cc_start: 0.7957 (t70) cc_final: 0.7538 (t0) REVERT: C 984 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7159 (t80) REVERT: C 1026 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8214 (ttpp) REVERT: C 1071 TYR cc_start: 0.8823 (m-80) cc_final: 0.8411 (m-80) outliers start: 51 outliers final: 39 residues processed: 273 average time/residue: 0.1594 time to fit residues: 71.2744 Evaluate side-chains 260 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 80 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 306 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS A1059 ASN B 282 ASN B 295 GLN B 445 ASN B 979 GLN B 996 GLN B1051 GLN C 187 ASN C 270 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108096 restraints weight = 36124.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110639 restraints weight = 23431.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112307 restraints weight = 17862.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113345 restraints weight = 15080.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113946 restraints weight = 13574.339| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 27474 Z= 0.254 Angle : 0.656 11.111 37488 Z= 0.327 Chirality : 0.047 0.321 4620 Planarity : 0.004 0.043 4584 Dihedral : 6.562 59.767 5542 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.48 % Allowed : 10.99 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3177 helix: 1.65 (0.19), residues: 744 sheet: 0.34 (0.18), residues: 738 loop : -0.89 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1090 TYR 0.021 0.002 TYR A 652 PHE 0.018 0.002 PHE C 39 TRP 0.009 0.002 TRP C 189 HIS 0.008 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00614 (27336) covalent geometry : angle 0.62763 (37116) SS BOND : bond 0.00519 ( 42) SS BOND : angle 1.48937 ( 84) hydrogen bonds : bond 0.05176 ( 1099) hydrogen bonds : angle 5.33173 ( 3063) link_ALPHA1-2 : bond 0.00253 ( 3) link_ALPHA1-2 : angle 1.35157 ( 9) link_ALPHA1-3 : bond 0.01277 ( 3) link_ALPHA1-3 : angle 1.37367 ( 9) link_ALPHA1-6 : bond 0.01192 ( 6) link_ALPHA1-6 : angle 2.59686 ( 18) link_BETA1-2 : bond 0.00042 ( 3) link_BETA1-2 : angle 3.29941 ( 9) link_BETA1-4 : bond 0.00418 ( 36) link_BETA1-4 : angle 1.39034 ( 108) link_NAG-ASN : bond 0.00656 ( 45) link_NAG-ASN : angle 2.53376 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 226 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.7943 (m-80) cc_final: 0.7739 (m-80) REVERT: A 214 MET cc_start: 0.8140 (tmm) cc_final: 0.6738 (tmm) REVERT: A 899 ASP cc_start: 0.8293 (t70) cc_final: 0.7790 (t0) REVERT: A 1051 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7448 (mt0) REVERT: A 1124 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8961 (mttm) REVERT: B 545 ASP cc_start: 0.7688 (m-30) cc_final: 0.7391 (t0) REVERT: B 899 ASP cc_start: 0.8295 (t70) cc_final: 0.7776 (t0) REVERT: B 984 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 545 ASP cc_start: 0.7616 (m-30) cc_final: 0.7316 (t0) REVERT: C 899 ASP cc_start: 0.8157 (t70) cc_final: 0.7679 (t0) REVERT: C 984 TYR cc_start: 0.7804 (m-80) cc_final: 0.7328 (t80) REVERT: C 1061 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8077 (mm110) REVERT: C 1082 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7748 (mt0) outliers start: 71 outliers final: 58 residues processed: 282 average time/residue: 0.1625 time to fit residues: 75.2281 Evaluate side-chains 277 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 83 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS B 571 ASN B1061 GLN C 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101281 restraints weight = 36755.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102388 restraints weight = 25736.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103194 restraints weight = 20809.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104262 restraints weight = 17877.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104413 restraints weight = 16991.509| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27474 Z= 0.167 Angle : 0.578 12.475 37488 Z= 0.288 Chirality : 0.044 0.243 4620 Planarity : 0.003 0.044 4584 Dihedral : 6.369 59.884 5542 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.99 % Allowed : 11.97 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3177 helix: 1.84 (0.19), residues: 744 sheet: 0.38 (0.19), residues: 720 loop : -0.87 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1090 TYR 0.022 0.001 TYR A 407 PHE 0.021 0.001 PHE A 35 TRP 0.009 0.001 TRP C 168 HIS 0.004 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00391 (27336) covalent geometry : angle 0.55150 (37116) SS BOND : bond 0.00435 ( 42) SS BOND : angle 1.29910 ( 84) hydrogen bonds : bond 0.04584 ( 1099) hydrogen bonds : angle 5.17574 ( 3063) link_ALPHA1-2 : bond 0.00272 ( 3) link_ALPHA1-2 : angle 1.33049 ( 9) link_ALPHA1-3 : bond 0.01218 ( 3) link_ALPHA1-3 : angle 1.24431 ( 9) link_ALPHA1-6 : bond 0.01233 ( 6) link_ALPHA1-6 : angle 2.43635 ( 18) link_BETA1-2 : bond 0.00236 ( 3) link_BETA1-2 : angle 2.52158 ( 9) link_BETA1-4 : bond 0.00412 ( 36) link_BETA1-4 : angle 1.32352 ( 108) link_NAG-ASN : bond 0.00471 ( 45) link_NAG-ASN : angle 2.31004 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8146 (tmm) cc_final: 0.6901 (tmm) REVERT: A 899 ASP cc_start: 0.8187 (t70) cc_final: 0.7700 (t0) REVERT: A 1051 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7424 (mt0) REVERT: A 1124 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8933 (mttm) REVERT: B 111 LYS cc_start: 0.6153 (pttm) cc_final: 0.5707 (tptt) REVERT: B 545 ASP cc_start: 0.7780 (m-30) cc_final: 0.7471 (t0) REVERT: B 899 ASP cc_start: 0.8080 (t70) cc_final: 0.7565 (t0) REVERT: B 984 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 1209 MET cc_start: 0.8758 (mtt) cc_final: 0.8543 (mtt) REVERT: C 214 MET cc_start: 0.7650 (ttp) cc_final: 0.7360 (tmm) REVERT: C 899 ASP cc_start: 0.7957 (t70) cc_final: 0.7527 (t0) REVERT: C 984 TYR cc_start: 0.7694 (m-80) cc_final: 0.7274 (t80) outliers start: 57 outliers final: 50 residues processed: 267 average time/residue: 0.1609 time to fit residues: 71.2676 Evaluate side-chains 268 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 223 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 248 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 988 GLN B1192 HIS C1061 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106998 restraints weight = 36255.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109599 restraints weight = 23324.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111247 restraints weight = 17636.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112340 restraints weight = 14859.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112912 restraints weight = 13337.403| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27474 Z= 0.148 Angle : 0.559 12.047 37488 Z= 0.280 Chirality : 0.044 0.219 4620 Planarity : 0.003 0.043 4584 Dihedral : 6.185 57.303 5542 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 12.01 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3177 helix: 1.94 (0.19), residues: 744 sheet: 0.39 (0.19), residues: 720 loop : -0.85 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1090 TYR 0.019 0.001 TYR C 407 PHE 0.019 0.001 PHE A 176 TRP 0.009 0.001 TRP C 168 HIS 0.004 0.001 HIS B1155 Details of bonding type rmsd covalent geometry : bond 0.00345 (27336) covalent geometry : angle 0.53483 (37116) SS BOND : bond 0.00409 ( 42) SS BOND : angle 1.17267 ( 84) hydrogen bonds : bond 0.04407 ( 1099) hydrogen bonds : angle 5.10395 ( 3063) link_ALPHA1-2 : bond 0.00259 ( 3) link_ALPHA1-2 : angle 1.35832 ( 9) link_ALPHA1-3 : bond 0.01222 ( 3) link_ALPHA1-3 : angle 1.22255 ( 9) link_ALPHA1-6 : bond 0.01169 ( 6) link_ALPHA1-6 : angle 2.35614 ( 18) link_BETA1-2 : bond 0.00233 ( 3) link_BETA1-2 : angle 2.52618 ( 9) link_BETA1-4 : bond 0.00429 ( 36) link_BETA1-4 : angle 1.30204 ( 108) link_NAG-ASN : bond 0.00429 ( 45) link_NAG-ASN : angle 2.15388 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8120 (tmm) cc_final: 0.6992 (tmm) REVERT: A 1124 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8934 (mttm) REVERT: B 38 LYS cc_start: 0.7847 (mttp) cc_final: 0.7185 (mtpp) REVERT: B 111 LYS cc_start: 0.6112 (pttm) cc_final: 0.5689 (tptt) REVERT: B 545 ASP cc_start: 0.7688 (m-30) cc_final: 0.7413 (t0) REVERT: B 899 ASP cc_start: 0.8126 (t70) cc_final: 0.7640 (t0) REVERT: B 984 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 1124 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9148 (mtpp) REVERT: C 38 LYS cc_start: 0.7952 (mttp) cc_final: 0.7397 (mtpt) REVERT: C 111 LYS cc_start: 0.6344 (pttm) cc_final: 0.5930 (tptt) REVERT: C 397 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: C 899 ASP cc_start: 0.8003 (t70) cc_final: 0.7591 (t0) REVERT: C 984 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.7256 (t80) REVERT: C 1071 TYR cc_start: 0.8787 (m-80) cc_final: 0.8419 (m-80) outliers start: 59 outliers final: 49 residues processed: 269 average time/residue: 0.1611 time to fit residues: 71.5264 Evaluate side-chains 268 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 119 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 84 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106652 restraints weight = 36183.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109212 restraints weight = 23375.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110895 restraints weight = 17754.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111964 restraints weight = 14926.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112523 restraints weight = 13388.044| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27474 Z= 0.158 Angle : 0.573 12.057 37488 Z= 0.285 Chirality : 0.044 0.478 4620 Planarity : 0.003 0.043 4584 Dihedral : 6.210 57.000 5542 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.06 % Allowed : 12.15 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3177 helix: 1.93 (0.19), residues: 747 sheet: 0.51 (0.19), residues: 747 loop : -0.90 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1090 TYR 0.021 0.001 TYR C 407 PHE 0.025 0.001 PHE A 35 TRP 0.008 0.001 TRP C 259 HIS 0.004 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00371 (27336) covalent geometry : angle 0.54534 (37116) SS BOND : bond 0.00413 ( 42) SS BOND : angle 1.17847 ( 84) hydrogen bonds : bond 0.04446 ( 1099) hydrogen bonds : angle 5.10232 ( 3063) link_ALPHA1-2 : bond 0.00306 ( 3) link_ALPHA1-2 : angle 1.36828 ( 9) link_ALPHA1-3 : bond 0.01225 ( 3) link_ALPHA1-3 : angle 1.26924 ( 9) link_ALPHA1-6 : bond 0.01136 ( 6) link_ALPHA1-6 : angle 2.33283 ( 18) link_BETA1-2 : bond 0.00225 ( 3) link_BETA1-2 : angle 2.55902 ( 9) link_BETA1-4 : bond 0.00430 ( 36) link_BETA1-4 : angle 1.34027 ( 108) link_NAG-ASN : bond 0.00570 ( 45) link_NAG-ASN : angle 2.38689 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8087 (tmm) cc_final: 0.6958 (tmm) REVERT: A 263 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8742 (p) REVERT: A 899 ASP cc_start: 0.8153 (t0) cc_final: 0.7865 (t0) REVERT: A 1124 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8940 (mttm) REVERT: B 38 LYS cc_start: 0.7845 (mttp) cc_final: 0.7166 (mtpp) REVERT: B 545 ASP cc_start: 0.7624 (m-30) cc_final: 0.7347 (t0) REVERT: B 899 ASP cc_start: 0.8119 (t70) cc_final: 0.7607 (t0) REVERT: B 984 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.7129 (t80) REVERT: B 1124 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9148 (mtpp) REVERT: C 397 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: C 708 TYR cc_start: 0.9153 (t80) cc_final: 0.8935 (t80) REVERT: C 899 ASP cc_start: 0.8036 (t70) cc_final: 0.7617 (t0) REVERT: C 984 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7264 (t80) outliers start: 59 outliers final: 50 residues processed: 268 average time/residue: 0.1657 time to fit residues: 72.2954 Evaluate side-chains 275 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 961 MET Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 125 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 286 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN C1192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100591 restraints weight = 36465.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102845 restraints weight = 24193.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104310 restraints weight = 18626.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105132 restraints weight = 15821.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105839 restraints weight = 14338.836| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27474 Z= 0.122 Angle : 0.543 11.546 37488 Z= 0.270 Chirality : 0.044 0.476 4620 Planarity : 0.003 0.044 4584 Dihedral : 6.016 55.644 5542 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.02 % Allowed : 12.43 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3177 helix: 2.10 (0.19), residues: 747 sheet: 0.49 (0.19), residues: 717 loop : -0.85 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1090 TYR 0.018 0.001 TYR C 407 PHE 0.022 0.001 PHE A 35 TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00275 (27336) covalent geometry : angle 0.51682 (37116) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.07148 ( 84) hydrogen bonds : bond 0.04146 ( 1099) hydrogen bonds : angle 4.98813 ( 3063) link_ALPHA1-2 : bond 0.00305 ( 3) link_ALPHA1-2 : angle 1.37355 ( 9) link_ALPHA1-3 : bond 0.01187 ( 3) link_ALPHA1-3 : angle 1.21471 ( 9) link_ALPHA1-6 : bond 0.01144 ( 6) link_ALPHA1-6 : angle 2.23650 ( 18) link_BETA1-2 : bond 0.00292 ( 3) link_BETA1-2 : angle 2.36394 ( 9) link_BETA1-4 : bond 0.00449 ( 36) link_BETA1-4 : angle 1.28139 ( 108) link_NAG-ASN : bond 0.00522 ( 45) link_NAG-ASN : angle 2.24474 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3858.74 seconds wall clock time: 67 minutes 53.30 seconds (4073.30 seconds total)