Starting phenix.real_space_refine on Tue Jun 24 06:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d5a_27207/06_2025/8d5a_27207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d5a_27207/06_2025/8d5a_27207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d5a_27207/06_2025/8d5a_27207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d5a_27207/06_2025/8d5a_27207.map" model { file = "/net/cci-nas-00/data/ceres_data/8d5a_27207/06_2025/8d5a_27207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d5a_27207/06_2025/8d5a_27207.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.011 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 120 5.16 5 C 17622 2.51 5 N 4487 2.21 5 O 5482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 171 residue(s): 2.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27711 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8773 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 52, 'TRANS': 1065} Chain breaks: 4 Chain: "B" Number of atoms: 8822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8822 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 52, 'TRANS': 1072} Chain breaks: 3 Chain: "C" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8796 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 18.15, per 1000 atoms: 0.65 Number of scatterers: 27711 At special positions: 0 Unit cell: (146.08, 151.06, 205.84, 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 120 16.00 O 5482 8.00 N 4487 7.00 C 17622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.99 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.00 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG F 2 " - " MAN F 3 " " NAG H 2 " - " MAN H 3 " " NAG I 2 " - " MAN I 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG Z 2 " - " MAN Z 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 331 " " NAG C1403 " - " ASN C 603 " " NAG C1404 " - " ASN C 657 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C1158 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 282 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1074 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.43 Conformation dependent library (CDL) restraints added in 3.6 seconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 45 sheets defined 27.1% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.619A pdb=" N LEU A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.602A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.802A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.735A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.593A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.544A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.971A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.743A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.449A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.803A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.313A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.580A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.336A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.452A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.569A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.248A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.248A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.762A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.842A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.680A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.203A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.885A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.713A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.913A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.543A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.657A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.310A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.665A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.654A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1159 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.123A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 403 through 411 removed outlier: 4.626A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.829A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 removed outlier: 3.610A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.337A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.677A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.687A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.716A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.845A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.589A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 31 removed outlier: 3.533A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.617A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.813A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.772A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.134A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.178A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.178A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.834A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.022A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.644A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.765A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.253A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 20 through 31 removed outlier: 3.760A pdb=" N HIS B 66 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.672A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.817A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 141 through 146 removed outlier: 8.445A pdb=" N ASP B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.547A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.111A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.970A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.153A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.735A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.517A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.403A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 20 through 31 removed outlier: 3.527A pdb=" N THR C 20 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 68 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.669A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.357A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.641A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.386A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.176A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.176A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.555A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.889A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 1112 hydrogen bonds defined for protein. 3042 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: 14.90 Time building geometry restraints manager: 9.83 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: 5166 1.32 - 1.45: 7390 1.45 - 1.58: 15630 1.58 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 28336 Sorted by residual: bond pdb=" N PHE A 490 " pdb=" CA PHE A 490 " ideal model delta sigma weight residual 1.457 1.542 -0.085 1.41e-02 5.03e+03 3.61e+01 bond pdb=" C PHE A 490 " pdb=" N PRO A 491 " ideal model delta sigma weight residual 1.331 1.400 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA VAL B 620 " pdb=" C VAL B 620 " ideal model delta sigma weight residual 1.520 1.562 -0.042 8.80e-03 1.29e+04 2.27e+01 bond pdb=" C5 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C5 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.413 1.505 -0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 28331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 33403 2.97 - 5.94: 4881 5.94 - 8.91: 235 8.91 - 11.87: 14 11.87 - 14.84: 4 Bond angle restraints: 38537 Sorted by residual: angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 108.34 123.18 -14.84 1.64e+00 3.72e-01 8.19e+01 angle pdb=" OD1 ASN C 331 " pdb=" CG ASN C 331 " pdb=" ND2 ASN C 331 " ideal model delta sigma weight residual 122.60 113.60 9.00 1.00e+00 1.00e+00 8.09e+01 angle pdb=" C ASP A 215 " pdb=" N LEU A 216 " pdb=" CA LEU A 216 " ideal model delta sigma weight residual 122.28 129.94 -7.66 8.80e-01 1.29e+00 7.57e+01 angle pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " pdb=" CG ASN B 709 " ideal model delta sigma weight residual 112.60 120.60 -8.00 1.00e+00 1.00e+00 6.40e+01 angle pdb=" N ARG A 34 " pdb=" CA ARG A 34 " pdb=" C ARG A 34 " ideal model delta sigma weight residual 110.53 120.95 -10.42 1.32e+00 5.74e-01 6.23e+01 ... (remaining 38532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 17141 24.73 - 49.46: 725 49.46 - 74.19: 163 74.19 - 98.91: 45 98.91 - 123.64: 52 Dihedral angle restraints: 18126 sinusoidal: 8316 harmonic: 9810 Sorted by residual: dihedral pdb=" C CYS B 617 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual -122.60 -140.64 18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual 122.80 139.82 -17.02 0 2.50e+00 1.60e-01 4.64e+01 dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 18123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 4601 0.368 - 0.737: 24 0.737 - 1.105: 2 1.105 - 1.474: 2 1.474 - 1.842: 2 Chirality restraints: 4631 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 ... (remaining 4628 not shown) Planarity restraints: 4883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.170 2.00e-02 2.50e+03 2.06e-01 5.29e+02 pdb=" CG ASN B 709 " 0.103 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.338 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " -0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.156 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 709 " 0.109 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.297 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.020 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" CG ASN A 603 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.176 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.319 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " 0.186 2.00e-02 2.50e+03 ... (remaining 4880 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 22 2.25 - 2.91: 10520 2.91 - 3.58: 37530 3.58 - 4.24: 63706 4.24 - 4.90: 106777 Nonbonded interactions: 218555 Sorted by model distance: nonbonded pdb=" CG2 THR A 20 " pdb=" OD2 ASP A 80 " model vdw 1.589 3.460 nonbonded pdb=" CE1 PHE C 559 " pdb=" CG2 ILE C 584 " model vdw 1.646 3.760 nonbonded pdb=" CZ PHE C 559 " pdb=" CG2 ILE C 584 " model vdw 1.685 3.760 nonbonded pdb=" OH TYR C 453 " pdb=" CD2 LEU C 492 " model vdw 1.903 3.460 nonbonded pdb=" O MET C 900 " pdb=" CD1 TYR C 904 " model vdw 1.925 3.340 ... (remaining 218550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 624 or resid 631 through 1162 or resid 1401 thr \ ough 1406)) selection = (chain 'B' and (resid 14 through 624 or resid 631 through 827 or resid 832 throu \ gh 1162 or resid 1401 through 1406)) selection = (chain 'C' and (resid 14 through 71 or resid 80 through 624 or resid 631 through \ 827 or resid 832 through 1162 or resid 1401 through 1406)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.310 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: 0.040 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 71.070 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 0.541 28481 Z= 1.013 Angle : 2.063 27.902 38924 Z= 1.316 Chirality : 0.129 1.842 4631 Planarity : 0.014 0.124 4834 Dihedral : 16.442 123.642 11689 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 1.62 % Allowed : 6.68 % Favored : 91.70 % Rotamer: Outliers : 2.22 % Allowed : 6.14 % Favored : 91.64 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3339 helix: -1.90 (0.15), residues: 777 sheet: 0.10 (0.20), residues: 601 loop : -1.82 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.025 TRP B 104 HIS 0.035 0.008 HIS A 69 PHE 0.114 0.016 PHE B 497 TYR 0.118 0.022 TYR C 449 ARG 0.028 0.002 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.11981 ( 49) link_NAG-ASN : angle 7.81473 ( 147) link_ALPHA1-4 : bond 0.02641 ( 18) link_ALPHA1-4 : angle 3.74978 ( 54) link_BETA1-4 : bond 0.02470 ( 29) link_BETA1-4 : angle 4.18396 ( 87) hydrogen bonds : bond 0.17328 ( 1090) hydrogen bonds : angle 8.94421 ( 3042) link_BETA1-6 : bond 0.03773 ( 3) link_BETA1-6 : angle 2.41145 ( 9) SS BOND : bond 0.01542 ( 45) SS BOND : angle 2.64217 ( 90) covalent geometry : bond 0.01625 (28336) covalent geometry : angle 1.99751 (38537) Misc. bond : bond 0.52794 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7587 (m) REVERT: A 152 TRP cc_start: 0.8752 (m100) cc_final: 0.7783 (m100) REVERT: A 429 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 814 LYS cc_start: 0.9118 (mttt) cc_final: 0.8852 (mmtt) REVERT: A 1029 MET cc_start: 0.9543 (tpp) cc_final: 0.9201 (tpt) REVERT: B 374 PHE cc_start: 0.7595 (p90) cc_final: 0.6898 (p90) REVERT: B 394 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 634 ARG cc_start: 0.7289 (ttp80) cc_final: 0.6558 (ttp80) REVERT: B 988 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: C 54 LEU cc_start: 0.8884 (mt) cc_final: 0.8648 (mt) REVERT: C 104 TRP cc_start: 0.6691 (m-90) cc_final: 0.6270 (m-90) REVERT: C 117 LEU cc_start: 0.7584 (tt) cc_final: 0.7155 (mm) REVERT: C 391 CYS cc_start: -0.2473 (OUTLIER) cc_final: -0.4090 (p) outliers start: 65 outliers final: 16 residues processed: 230 average time/residue: 0.4293 time to fit residues: 156.2896 Evaluate side-chains 108 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 914 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 183 GLN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN B 52 GLN B 183 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 409 GLN B 448 ASN B 450 ASN B 460 ASN B 506 GLN B 519 HIS B 762 GLN B 955 ASN B1002 GLN C 450 ASN C 762 GLN C 955 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.101997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064145 restraints weight = 78922.324| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.33 r_work: 0.3004 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28481 Z= 0.166 Angle : 0.829 15.311 38924 Z= 0.399 Chirality : 0.050 0.745 4631 Planarity : 0.005 0.073 4834 Dihedral : 13.183 114.185 5694 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.61 % Favored : 94.97 % Rotamer: Outliers : 1.88 % Allowed : 8.67 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3339 helix: 0.24 (0.18), residues: 793 sheet: 0.19 (0.19), residues: 702 loop : -1.56 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 633 HIS 0.005 0.001 HIS B1048 PHE 0.030 0.002 PHE B 374 TYR 0.027 0.002 TYR A 160 ARG 0.007 0.001 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00812 ( 49) link_NAG-ASN : angle 4.42344 ( 147) link_ALPHA1-4 : bond 0.01468 ( 18) link_ALPHA1-4 : angle 2.74717 ( 54) link_BETA1-4 : bond 0.00390 ( 29) link_BETA1-4 : angle 1.92883 ( 87) hydrogen bonds : bond 0.04561 ( 1090) hydrogen bonds : angle 6.48719 ( 3042) link_BETA1-6 : bond 0.01235 ( 3) link_BETA1-6 : angle 1.82228 ( 9) SS BOND : bond 0.00334 ( 45) SS BOND : angle 1.49708 ( 90) covalent geometry : bond 0.00353 (28336) covalent geometry : angle 0.77094 (38537) Misc. bond : bond 0.01016 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.8172 (m100) cc_final: 0.7958 (m100) REVERT: A 429 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7359 (t80) REVERT: A 814 LYS cc_start: 0.9175 (mttt) cc_final: 0.8839 (mmtt) REVERT: A 867 ASP cc_start: 0.8749 (m-30) cc_final: 0.8268 (p0) REVERT: B 394 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (p0) REVERT: B 634 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6330 (ttp80) REVERT: B 902 MET cc_start: 0.9092 (mmt) cc_final: 0.8819 (mmt) REVERT: B 988 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: C 102 ARG cc_start: 0.6692 (mmt180) cc_final: 0.6011 (mmp-170) REVERT: C 565 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6159 (p90) outliers start: 55 outliers final: 27 residues processed: 153 average time/residue: 0.3899 time to fit residues: 97.5810 Evaluate side-chains 115 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 96 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN A1083 HIS B1005 GLN C 66 HIS C 121 ASN C 519 HIS C 804 GLN C 914 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.101710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063986 restraints weight = 78908.046| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.31 r_work: 0.3000 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28481 Z= 0.139 Angle : 0.727 13.504 38924 Z= 0.340 Chirality : 0.047 0.553 4631 Planarity : 0.004 0.079 4834 Dihedral : 11.736 111.370 5682 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.15 % Favored : 94.49 % Rotamer: Outliers : 2.08 % Allowed : 9.04 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3339 helix: 0.91 (0.18), residues: 796 sheet: 0.36 (0.19), residues: 703 loop : -1.41 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 633 HIS 0.006 0.001 HIS B 245 PHE 0.026 0.001 PHE C 855 TYR 0.020 0.001 TYR C 495 ARG 0.017 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 49) link_NAG-ASN : angle 3.91597 ( 147) link_ALPHA1-4 : bond 0.01597 ( 18) link_ALPHA1-4 : angle 2.76581 ( 54) link_BETA1-4 : bond 0.00330 ( 29) link_BETA1-4 : angle 1.44861 ( 87) hydrogen bonds : bond 0.03991 ( 1090) hydrogen bonds : angle 5.88939 ( 3042) link_BETA1-6 : bond 0.01580 ( 3) link_BETA1-6 : angle 1.83121 ( 9) SS BOND : bond 0.00270 ( 45) SS BOND : angle 1.09127 ( 90) covalent geometry : bond 0.00297 (28336) covalent geometry : angle 0.67524 (38537) Misc. bond : bond 0.00260 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 98 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 152 TRP cc_start: 0.8305 (m100) cc_final: 0.8031 (m100) REVERT: A 190 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: A 429 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7154 (t80) REVERT: A 814 LYS cc_start: 0.9187 (mttt) cc_final: 0.8860 (mmtt) REVERT: A 867 ASP cc_start: 0.8671 (m-30) cc_final: 0.8228 (p0) REVERT: B 455 LEU cc_start: 0.8505 (tp) cc_final: 0.8263 (tt) REVERT: B 634 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6257 (ttp80) REVERT: B 823 PHE cc_start: 0.9133 (t80) cc_final: 0.8925 (t80) REVERT: B 902 MET cc_start: 0.9123 (mmt) cc_final: 0.8842 (mmt) REVERT: B 988 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: C 102 ARG cc_start: 0.6699 (mmt180) cc_final: 0.5979 (mmp-170) outliers start: 61 outliers final: 33 residues processed: 151 average time/residue: 0.3599 time to fit residues: 91.7729 Evaluate side-chains 121 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 325 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 310 optimal weight: 0.6980 chunk 305 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN C 460 ASN C 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.099144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060730 restraints weight = 80087.025| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.33 r_work: 0.2920 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 28481 Z= 0.261 Angle : 0.771 13.820 38924 Z= 0.361 Chirality : 0.048 0.542 4631 Planarity : 0.004 0.076 4834 Dihedral : 10.845 111.706 5673 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.09 % Favored : 94.58 % Rotamer: Outliers : 2.18 % Allowed : 9.80 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3339 helix: 0.89 (0.18), residues: 798 sheet: 0.17 (0.19), residues: 729 loop : -1.52 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS C1064 PHE 0.020 0.002 PHE C 855 TYR 0.022 0.002 TYR C 495 ARG 0.007 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 49) link_NAG-ASN : angle 3.91769 ( 147) link_ALPHA1-4 : bond 0.01604 ( 18) link_ALPHA1-4 : angle 3.19357 ( 54) link_BETA1-4 : bond 0.00705 ( 29) link_BETA1-4 : angle 1.71842 ( 87) hydrogen bonds : bond 0.04366 ( 1090) hydrogen bonds : angle 5.89184 ( 3042) link_BETA1-6 : bond 0.01451 ( 3) link_BETA1-6 : angle 2.09067 ( 9) SS BOND : bond 0.00418 ( 45) SS BOND : angle 1.26744 ( 90) covalent geometry : bond 0.00608 (28336) covalent geometry : angle 0.71891 (38537) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 89 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 152 TRP cc_start: 0.8353 (m100) cc_final: 0.8133 (m100) REVERT: A 429 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 633 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.7626 (p-90) REVERT: A 636 TYR cc_start: 0.7080 (m-80) cc_final: 0.6807 (m-80) REVERT: A 675 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8484 (pp30) REVERT: A 814 LYS cc_start: 0.9208 (mttt) cc_final: 0.8868 (mmtt) REVERT: A 867 ASP cc_start: 0.8736 (m-30) cc_final: 0.8266 (p0) REVERT: B 633 TRP cc_start: 0.9154 (OUTLIER) cc_final: 0.8727 (p-90) REVERT: B 634 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6237 (ttp80) REVERT: B 636 TYR cc_start: 0.6413 (m-80) cc_final: 0.6193 (m-80) REVERT: B 988 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: C 351 TYR cc_start: 0.5382 (OUTLIER) cc_final: 0.4949 (p90) REVERT: C 425 LEU cc_start: -0.2661 (OUTLIER) cc_final: -0.3011 (pp) outliers start: 64 outliers final: 34 residues processed: 145 average time/residue: 0.3463 time to fit residues: 86.8586 Evaluate side-chains 124 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 296 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 chunk 288 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 116 optimal weight: 50.0000 chunk 279 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.100970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063433 restraints weight = 79052.656| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.21 r_work: 0.2989 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28481 Z= 0.125 Angle : 0.684 13.199 38924 Z= 0.315 Chirality : 0.045 0.434 4631 Planarity : 0.004 0.079 4834 Dihedral : 10.136 108.646 5673 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.46 % Favored : 95.24 % Rotamer: Outliers : 2.01 % Allowed : 10.51 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3339 helix: 1.21 (0.19), residues: 803 sheet: 0.29 (0.19), residues: 716 loop : -1.40 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.001 PHE C 855 TYR 0.020 0.001 TYR C 495 ARG 0.006 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 49) link_NAG-ASN : angle 3.85610 ( 147) link_ALPHA1-4 : bond 0.01667 ( 18) link_ALPHA1-4 : angle 2.92520 ( 54) link_BETA1-4 : bond 0.00336 ( 29) link_BETA1-4 : angle 1.30023 ( 87) hydrogen bonds : bond 0.03594 ( 1090) hydrogen bonds : angle 5.54459 ( 3042) link_BETA1-6 : bond 0.01481 ( 3) link_BETA1-6 : angle 2.12017 ( 9) SS BOND : bond 0.00414 ( 45) SS BOND : angle 1.02348 ( 90) covalent geometry : bond 0.00262 (28336) covalent geometry : angle 0.62956 (38537) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 95 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8685 (mp) REVERT: A 177 MET cc_start: 0.8341 (ppp) cc_final: 0.8097 (ppp) REVERT: A 633 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.7688 (p-90) REVERT: A 636 TYR cc_start: 0.7055 (m-80) cc_final: 0.6837 (m-80) REVERT: A 675 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8498 (pp30) REVERT: A 814 LYS cc_start: 0.9172 (mttt) cc_final: 0.8859 (mmtt) REVERT: A 867 ASP cc_start: 0.8678 (m-30) cc_final: 0.8190 (p0) REVERT: B 375 PHE cc_start: 0.7668 (m-10) cc_final: 0.6975 (m-10) REVERT: B 417 ASN cc_start: 0.9327 (m-40) cc_final: 0.9017 (t0) REVERT: B 633 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.8741 (p-90) REVERT: B 634 ARG cc_start: 0.6887 (ttp80) cc_final: 0.6203 (ttp80) REVERT: B 830 ASP cc_start: 0.8180 (t0) cc_final: 0.7578 (t70) REVERT: B 988 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8492 (pm20) REVERT: C 351 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.4821 (p90) outliers start: 59 outliers final: 37 residues processed: 145 average time/residue: 0.3406 time to fit residues: 85.8995 Evaluate side-chains 128 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 245 optimal weight: 20.0000 chunk 290 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 306 optimal weight: 0.9980 chunk 314 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 248 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.100114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062301 restraints weight = 79446.506| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.26 r_work: 0.2961 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28481 Z= 0.161 Angle : 0.687 12.953 38924 Z= 0.317 Chirality : 0.045 0.447 4631 Planarity : 0.004 0.075 4834 Dihedral : 9.603 106.922 5671 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.70 % Favored : 95.00 % Rotamer: Outliers : 2.15 % Allowed : 10.75 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3339 helix: 1.16 (0.18), residues: 814 sheet: 0.24 (0.19), residues: 731 loop : -1.33 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 152 HIS 0.008 0.001 HIS A 146 PHE 0.018 0.001 PHE B 338 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 49) link_NAG-ASN : angle 3.70624 ( 147) link_ALPHA1-4 : bond 0.01586 ( 18) link_ALPHA1-4 : angle 3.07776 ( 54) link_BETA1-4 : bond 0.00248 ( 29) link_BETA1-4 : angle 1.44556 ( 87) hydrogen bonds : bond 0.03656 ( 1090) hydrogen bonds : angle 5.46139 ( 3042) link_BETA1-6 : bond 0.01417 ( 3) link_BETA1-6 : angle 2.21711 ( 9) SS BOND : bond 0.00263 ( 45) SS BOND : angle 1.27025 ( 90) covalent geometry : bond 0.00366 (28336) covalent geometry : angle 0.63362 (38537) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 91 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 135 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: A 177 MET cc_start: 0.8493 (ppp) cc_final: 0.7601 (ppp) REVERT: A 190 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7658 (mtp-110) REVERT: A 571 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7896 (t0) REVERT: A 633 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.7648 (p-90) REVERT: A 634 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.6175 (mmm160) REVERT: A 675 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8502 (pp30) REVERT: A 814 LYS cc_start: 0.9165 (mttt) cc_final: 0.8854 (mmtt) REVERT: A 867 ASP cc_start: 0.8741 (m-30) cc_final: 0.8219 (p0) REVERT: B 417 ASN cc_start: 0.9321 (m-40) cc_final: 0.8917 (t0) REVERT: B 830 ASP cc_start: 0.8237 (t0) cc_final: 0.7728 (t70) REVERT: B 988 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: C 102 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6172 (mmp-170) REVERT: C 351 TYR cc_start: 0.5289 (OUTLIER) cc_final: 0.4795 (p90) REVERT: C 633 TRP cc_start: 0.8547 (OUTLIER) cc_final: 0.8218 (p-90) outliers start: 63 outliers final: 38 residues processed: 145 average time/residue: 0.3559 time to fit residues: 88.6044 Evaluate side-chains 137 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 0.0170 chunk 271 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 264 optimal weight: 30.0000 chunk 253 optimal weight: 5.9990 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 913 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.097806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059330 restraints weight = 80052.800| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 4.30 r_work: 0.2887 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 28481 Z= 0.319 Angle : 0.780 14.642 38924 Z= 0.367 Chirality : 0.049 0.552 4631 Planarity : 0.004 0.071 4834 Dihedral : 9.607 108.453 5671 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.90 % Favored : 93.80 % Rotamer: Outliers : 2.22 % Allowed : 11.30 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3339 helix: 0.86 (0.18), residues: 809 sheet: 0.10 (0.19), residues: 716 loop : -1.45 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 152 HIS 0.007 0.001 HIS C1064 PHE 0.023 0.002 PHE B 338 TYR 0.020 0.002 TYR C 756 ARG 0.004 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 49) link_NAG-ASN : angle 3.89087 ( 147) link_ALPHA1-4 : bond 0.01539 ( 18) link_ALPHA1-4 : angle 2.91196 ( 54) link_BETA1-4 : bond 0.00291 ( 29) link_BETA1-4 : angle 1.68231 ( 87) hydrogen bonds : bond 0.04456 ( 1090) hydrogen bonds : angle 5.81227 ( 3042) link_BETA1-6 : bond 0.01426 ( 3) link_BETA1-6 : angle 2.22511 ( 9) SS BOND : bond 0.00456 ( 45) SS BOND : angle 1.51409 ( 90) covalent geometry : bond 0.00743 (28336) covalent geometry : angle 0.72895 (38537) Misc. bond : bond 0.00160 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 85 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 135 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: A 190 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7800 (mtt-85) REVERT: A 571 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 633 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7733 (p-90) REVERT: A 636 TYR cc_start: 0.6998 (m-80) cc_final: 0.6729 (m-80) REVERT: A 675 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8400 (pp30) REVERT: A 814 LYS cc_start: 0.9196 (mttt) cc_final: 0.8851 (mmtt) REVERT: A 867 ASP cc_start: 0.8760 (m-30) cc_final: 0.8294 (p0) REVERT: B 189 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9335 (tt) REVERT: B 634 ARG cc_start: 0.6860 (ttp80) cc_final: 0.6159 (ttp80) REVERT: B 988 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: C 220 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7571 (t80) REVERT: C 351 TYR cc_start: 0.5242 (OUTLIER) cc_final: 0.4744 (p90) REVERT: C 633 TRP cc_start: 0.8553 (OUTLIER) cc_final: 0.8038 (p-90) REVERT: C 1155 TYR cc_start: 0.4281 (OUTLIER) cc_final: 0.3964 (m-10) outliers start: 65 outliers final: 40 residues processed: 140 average time/residue: 0.3555 time to fit residues: 84.1713 Evaluate side-chains 131 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 79 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 101 optimal weight: 0.5980 chunk 158 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 174 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 234 optimal weight: 0.0670 chunk 110 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 149 ASN A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.099988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062147 restraints weight = 79373.292| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.30 r_work: 0.2959 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28481 Z= 0.124 Angle : 0.665 13.330 38924 Z= 0.308 Chirality : 0.045 0.428 4631 Planarity : 0.004 0.073 4834 Dihedral : 9.208 106.671 5670 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.46 % Favored : 95.24 % Rotamer: Outliers : 1.74 % Allowed : 11.88 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3339 helix: 1.16 (0.18), residues: 813 sheet: 0.17 (0.19), residues: 715 loop : -1.34 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.001 PHE B 338 TYR 0.024 0.001 TYR C 904 ARG 0.008 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 49) link_NAG-ASN : angle 3.62851 ( 147) link_ALPHA1-4 : bond 0.01515 ( 18) link_ALPHA1-4 : angle 2.88483 ( 54) link_BETA1-4 : bond 0.00300 ( 29) link_BETA1-4 : angle 1.28374 ( 87) hydrogen bonds : bond 0.03595 ( 1090) hydrogen bonds : angle 5.46388 ( 3042) link_BETA1-6 : bond 0.01665 ( 3) link_BETA1-6 : angle 2.19428 ( 9) SS BOND : bond 0.00242 ( 45) SS BOND : angle 1.10667 ( 90) covalent geometry : bond 0.00266 (28336) covalent geometry : angle 0.61426 (38537) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 91 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 135 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: A 190 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7809 (mtt-85) REVERT: A 571 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7937 (t0) REVERT: A 633 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.7953 (p-90) REVERT: A 675 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8403 (pp30) REVERT: A 814 LYS cc_start: 0.9154 (mttt) cc_final: 0.8841 (mmtt) REVERT: A 867 ASP cc_start: 0.8690 (m-30) cc_final: 0.8206 (p0) REVERT: B 830 ASP cc_start: 0.8216 (t0) cc_final: 0.7758 (t70) REVERT: B 988 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: C 220 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7396 (t80) REVERT: C 351 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.4847 (p90) REVERT: C 633 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7981 (p-90) outliers start: 51 outliers final: 32 residues processed: 135 average time/residue: 0.3592 time to fit residues: 82.7429 Evaluate side-chains 127 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 104 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.099265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060961 restraints weight = 79836.425| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.39 r_work: 0.2933 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28481 Z= 0.182 Angle : 0.684 13.120 38924 Z= 0.316 Chirality : 0.045 0.461 4631 Planarity : 0.004 0.072 4834 Dihedral : 8.940 106.164 5670 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.15 % Favored : 94.55 % Rotamer: Outliers : 1.77 % Allowed : 11.91 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3339 helix: 1.22 (0.18), residues: 806 sheet: 0.19 (0.18), residues: 731 loop : -1.35 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 152 HIS 0.004 0.001 HIS B 245 PHE 0.019 0.001 PHE B 338 TYR 0.033 0.001 TYR C 904 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 49) link_NAG-ASN : angle 3.64214 ( 147) link_ALPHA1-4 : bond 0.01497 ( 18) link_ALPHA1-4 : angle 2.86169 ( 54) link_BETA1-4 : bond 0.00208 ( 29) link_BETA1-4 : angle 1.42527 ( 87) hydrogen bonds : bond 0.03717 ( 1090) hydrogen bonds : angle 5.44756 ( 3042) link_BETA1-6 : bond 0.01474 ( 3) link_BETA1-6 : angle 2.14877 ( 9) SS BOND : bond 0.00287 ( 45) SS BOND : angle 1.14050 ( 90) covalent geometry : bond 0.00418 (28336) covalent geometry : angle 0.63353 (38537) Misc. bond : bond 0.00120 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 84 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 135 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.5947 (m-80) REVERT: A 633 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.8077 (p-90) REVERT: A 675 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8397 (pp30) REVERT: A 814 LYS cc_start: 0.9173 (mttt) cc_final: 0.8863 (mmtt) REVERT: A 867 ASP cc_start: 0.8716 (m-30) cc_final: 0.8227 (p0) REVERT: B 830 ASP cc_start: 0.8252 (t0) cc_final: 0.7809 (t70) REVERT: B 988 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: C 220 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 351 TYR cc_start: 0.5264 (OUTLIER) cc_final: 0.4843 (p90) REVERT: C 633 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.8007 (p-90) REVERT: C 1155 TYR cc_start: 0.3983 (OUTLIER) cc_final: 0.3598 (m-10) outliers start: 52 outliers final: 36 residues processed: 129 average time/residue: 0.3699 time to fit residues: 82.1993 Evaluate side-chains 126 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 233 optimal weight: 10.0000 chunk 319 optimal weight: 0.5980 chunk 267 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.100856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063539 restraints weight = 79682.660| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.95 r_work: 0.3041 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28481 Z= 0.122 Angle : 0.646 12.724 38924 Z= 0.298 Chirality : 0.044 0.391 4631 Planarity : 0.004 0.073 4834 Dihedral : 8.588 103.585 5670 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.43 % Favored : 95.30 % Rotamer: Outliers : 1.57 % Allowed : 12.22 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3339 helix: 1.34 (0.19), residues: 816 sheet: 0.28 (0.19), residues: 699 loop : -1.28 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 PHE 0.019 0.001 PHE B 375 TYR 0.027 0.001 TYR C 904 ARG 0.004 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 49) link_NAG-ASN : angle 3.52301 ( 147) link_ALPHA1-4 : bond 0.01475 ( 18) link_ALPHA1-4 : angle 2.80788 ( 54) link_BETA1-4 : bond 0.00332 ( 29) link_BETA1-4 : angle 1.21185 ( 87) hydrogen bonds : bond 0.03317 ( 1090) hydrogen bonds : angle 5.26226 ( 3042) link_BETA1-6 : bond 0.01571 ( 3) link_BETA1-6 : angle 2.13967 ( 9) SS BOND : bond 0.00208 ( 45) SS BOND : angle 0.98117 ( 90) covalent geometry : bond 0.00269 (28336) covalent geometry : angle 0.59753 (38537) Misc. bond : bond 0.00058 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 633 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.8036 (p-90) REVERT: A 867 ASP cc_start: 0.8690 (m-30) cc_final: 0.8340 (p0) REVERT: B 830 ASP cc_start: 0.8016 (t0) cc_final: 0.7550 (t70) REVERT: B 988 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: C 220 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 351 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.4606 (p90) REVERT: C 633 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.7879 (p-90) outliers start: 46 outliers final: 35 residues processed: 125 average time/residue: 0.4402 time to fit residues: 94.8913 Evaluate side-chains 122 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 265 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 152 optimal weight: 0.0770 chunk 263 optimal weight: 0.0870 chunk 192 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.102266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063322 restraints weight = 80446.643| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.90 r_work: 0.3092 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28481 Z= 0.127 Angle : 0.647 12.601 38924 Z= 0.296 Chirality : 0.044 0.406 4631 Planarity : 0.004 0.068 4834 Dihedral : 8.217 101.873 5668 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.70 % Favored : 95.06 % Rotamer: Outliers : 1.57 % Allowed : 12.08 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3339 helix: 1.40 (0.19), residues: 816 sheet: 0.24 (0.19), residues: 723 loop : -1.26 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.001 PHE B 375 TYR 0.026 0.001 TYR C 904 ARG 0.007 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 49) link_NAG-ASN : angle 3.50301 ( 147) link_ALPHA1-4 : bond 0.01468 ( 18) link_ALPHA1-4 : angle 2.77516 ( 54) link_BETA1-4 : bond 0.00277 ( 29) link_BETA1-4 : angle 1.25647 ( 87) hydrogen bonds : bond 0.03320 ( 1090) hydrogen bonds : angle 5.21047 ( 3042) link_BETA1-6 : bond 0.01537 ( 3) link_BETA1-6 : angle 2.17651 ( 9) SS BOND : bond 0.00230 ( 45) SS BOND : angle 0.97307 ( 90) covalent geometry : bond 0.00281 (28336) covalent geometry : angle 0.59810 (38537) Misc. bond : bond 0.00065 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17835.12 seconds wall clock time: 309 minutes 11.59 seconds (18551.59 seconds total)