Starting phenix.real_space_refine on Fri Mar 6 02:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbl_24982/03_2026/7sbl_24982_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbl_24982/03_2026/7sbl_24982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sbl_24982/03_2026/7sbl_24982_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbl_24982/03_2026/7sbl_24982_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sbl_24982/03_2026/7sbl_24982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbl_24982/03_2026/7sbl_24982.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 17157 2.51 5 N 4385 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27026 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8615 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 52, 'TRANS': 1049} Chain breaks: 4 Chain: "B" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8472 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 5 Chain: "C" Number of atoms: 8637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8637 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 53, 'TRANS': 1049} Chain breaks: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.09, per 1000 atoms: 0.23 Number of scatterers: 27026 At special positions: 0 Unit cell: (146.037, 142.737, 216.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5367 8.00 N 4385 7.00 C 17157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.06 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 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 I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG b 1 " - " FUC b 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 149 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 331 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN B 282 " " NAG N 1 " - " ASN B 616 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 343 " " NAG U 1 " - " ASN B 165 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1074 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " " NAG e 1 " - " ASN C 343 " " NAG f 1 " - " ASN C 165 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 46 sheets defined 27.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 180 through 185 removed outlier: 4.429A pdb=" N ASN A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.602A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.879A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.642A pdb=" N ILE A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 411' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.023A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.509A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.624A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.909A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.652A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.930A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.278A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.127A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.139A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.376A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.017A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.503A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.784A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 638' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.875A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.089A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.630A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.537A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.127A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1159 removed outlier: 3.884A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B1152 " --> pdb=" O PHE B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.526A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.025A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.032A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.726A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.015A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.465A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.544A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.694A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.505A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.529A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.898A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.260A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C1152 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.858A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.640A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.668A 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: 5.948A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.834A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.551A 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: 6.846A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.763A 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: 6.584A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.596A 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: 6.584A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.182A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.133A 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 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.658A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 49 removed outlier: 7.472A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.480A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.299A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.170A 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: 4.169A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.983A 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: 3.974A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.875A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.568A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.498A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.083A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.907A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.254A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.484A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.915A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.167A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.456A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.985A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.183A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A 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=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.550A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.236A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.615A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 2973 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 3.24 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: 5129 1.32 - 1.45: 7299 1.45 - 1.58: 15042 1.58 - 1.71: 2 1.71 - 1.84: 147 Bond restraints: 27619 Sorted by residual: bond pdb=" CA ASN A 81 " pdb=" C ASN A 81 " ideal model delta sigma weight residual 1.524 1.586 -0.062 1.26e-02 6.30e+03 2.44e+01 bond pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 1.517 1.550 -0.033 6.70e-03 2.23e+04 2.43e+01 bond pdb=" C5 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " 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 A1409 " pdb=" O5 NAG A1409 " ideal model delta sigma weight residual 1.413 1.501 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 27614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 31397 2.56 - 5.11: 5722 5.11 - 7.67: 404 7.67 - 10.23: 31 10.23 - 12.78: 8 Bond angle restraints: 37562 Sorted by residual: angle pdb=" N ASN A 17 " pdb=" CA ASN A 17 " pdb=" C ASN A 17 " ideal model delta sigma weight residual 110.24 122.99 -12.75 1.41e+00 5.03e-01 8.18e+01 angle pdb=" N ASN C 17 " pdb=" CA ASN C 17 " pdb=" C ASN C 17 " ideal model delta sigma weight residual 110.23 123.01 -12.78 1.45e+00 4.76e-01 7.77e+01 angle pdb=" N ASN B 17 " pdb=" CA ASN B 17 " pdb=" C ASN B 17 " ideal model delta sigma weight residual 110.23 122.93 -12.70 1.45e+00 4.76e-01 7.67e+01 angle pdb=" N VAL A 143 " pdb=" CA VAL A 143 " pdb=" C VAL A 143 " ideal model delta sigma weight residual 108.89 98.80 10.09 1.32e+00 5.74e-01 5.84e+01 angle pdb=" N ARG A 19 " pdb=" CA ARG A 19 " pdb=" C ARG A 19 " ideal model delta sigma weight residual 110.68 100.07 10.61 1.39e+00 5.18e-01 5.83e+01 ... (remaining 37557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.23: 16937 25.23 - 50.46: 565 50.46 - 75.69: 128 75.69 - 100.92: 31 100.92 - 126.15: 34 Dihedral angle restraints: 17695 sinusoidal: 8130 harmonic: 9565 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -154.93 68.93 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" C ASN A 603 " pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta harmonic sigma weight residual -122.60 -141.47 18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" N ASN A 603 " pdb=" C ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta harmonic sigma weight residual 122.80 140.63 -17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 17692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 4467 0.339 - 0.678: 32 0.678 - 1.016: 10 1.016 - 1.355: 6 1.355 - 1.694: 3 Chirality restraints: 4518 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.33e+01 ... (remaining 4515 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.181 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" CG ASN B 343 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.300 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.181 2.00e-02 2.50e+03 1.95e-01 4.78e+02 pdb=" CG ASN A 343 " -0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.300 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.101 2.00e-02 2.50e+03 1.37e-01 2.36e+02 pdb=" CG ASN B 165 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.237 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.160 2.00e-02 2.50e+03 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1027 2.74 - 3.28: 27152 3.28 - 3.82: 40951 3.82 - 4.36: 54890 4.36 - 4.90: 88246 Nonbonded interactions: 212266 Sorted by model distance: nonbonded pdb=" N GLN A 23 " pdb=" OE1 GLN A 23 " model vdw 2.197 3.120 nonbonded pdb=" N GLU B 281 " pdb=" OE1 GLU B 281 " model vdw 2.210 3.120 nonbonded pdb=" N GLU A 154 " pdb=" OE1 GLU A 154 " model vdw 2.220 3.120 nonbonded pdb=" CB GLN C 173 " pdb=" CD PRO C 174 " model vdw 2.238 3.840 nonbonded pdb=" CG2 THR C 33 " pdb=" CE1 PHE C 58 " model vdw 2.255 3.760 ... (remaining 212261 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 828 or resid 854 through 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1407)) selection = (chain 'C' and (resid 14 through 623 or resid 636 through 828 or resid 854 throu \ gh 1407)) } ncs_group { reference = (chain 'D' 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 'Q' 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 '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) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'f' } 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: 10.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.780 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.014 0.095 27758 Z= 0.810 Angle : 2.020 43.792 37936 Z= 1.256 Chirality : 0.132 1.694 4518 Planarity : 0.013 0.124 4731 Dihedral : 14.917 126.149 11416 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.81 % Favored : 91.46 % Rotamer: Outliers : 2.72 % Allowed : 4.43 % Favored : 92.84 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 3254 helix: -1.41 (0.16), residues: 736 sheet: 0.31 (0.21), residues: 580 loop : -1.78 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 21 TYR 0.120 0.020 TYR C 489 PHE 0.107 0.015 PHE C 898 TRP 0.122 0.021 TRP C 353 HIS 0.017 0.006 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.01433 (27619) covalent geometry : angle 1.87619 (37562) SS BOND : bond 0.01350 ( 43) SS BOND : angle 2.05840 ( 86) hydrogen bonds : bond 0.18073 ( 1083) hydrogen bonds : angle 8.88679 ( 2973) link_ALPHA1-4 : bond 0.03024 ( 10) link_ALPHA1-4 : angle 4.66332 ( 30) link_BETA1-4 : bond 0.02030 ( 29) link_BETA1-4 : angle 3.80412 ( 87) link_BETA1-6 : bond 0.02603 ( 3) link_BETA1-6 : angle 2.45408 ( 9) link_NAG-ASN : bond 0.01662 ( 54) link_NAG-ASN : angle 11.16034 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 987 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8848 (t) cc_final: 0.8557 (m) REVERT: A 114 THR cc_start: 0.7769 (p) cc_final: 0.7527 (p) REVERT: A 271 GLN cc_start: 0.7640 (mt0) cc_final: 0.7094 (mt0) REVERT: A 320 VAL cc_start: 0.9002 (t) cc_final: 0.8706 (m) REVERT: A 362 VAL cc_start: 0.7353 (t) cc_final: 0.6904 (t) REVERT: A 505 TYR cc_start: 0.5791 (t80) cc_final: 0.5576 (t80) REVERT: A 533 LEU cc_start: 0.8657 (tp) cc_final: 0.8267 (tt) REVERT: A 571 ASP cc_start: 0.7577 (t0) cc_final: 0.7243 (t0) REVERT: A 697 MET cc_start: 0.8406 (ptm) cc_final: 0.8143 (ptm) REVERT: A 737 ASP cc_start: 0.8018 (t0) cc_final: 0.7524 (t0) REVERT: A 740 MET cc_start: 0.8777 (ttt) cc_final: 0.8568 (ttm) REVERT: A 745 ASP cc_start: 0.7173 (m-30) cc_final: 0.6745 (m-30) REVERT: A 818 ILE cc_start: 0.9295 (mt) cc_final: 0.9055 (mt) REVERT: A 904 TYR cc_start: 0.7788 (m-80) cc_final: 0.7450 (m-80) REVERT: A 985 ASP cc_start: 0.7406 (p0) cc_final: 0.6988 (p0) REVERT: B 62 VAL cc_start: 0.8650 (m) cc_final: 0.8445 (t) REVERT: B 96 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5207 (tp30) REVERT: B 128 ILE cc_start: 0.8248 (mt) cc_final: 0.7972 (mm) REVERT: B 178 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.4587 (m-30) REVERT: B 274 THR cc_start: 0.8850 (m) cc_final: 0.8130 (m) REVERT: B 329 PHE cc_start: 0.7814 (m-10) cc_final: 0.7560 (m-80) REVERT: B 396 TYR cc_start: 0.7707 (m-80) cc_final: 0.7011 (m-80) REVERT: B 696 THR cc_start: 0.9149 (m) cc_final: 0.8889 (p) REVERT: B 697 MET cc_start: 0.8427 (ptm) cc_final: 0.8089 (ptp) REVERT: B 808 ASP cc_start: 0.7841 (t0) cc_final: 0.7199 (t70) REVERT: B 824 ASN cc_start: 0.8664 (m-40) cc_final: 0.8438 (m-40) REVERT: B 976 VAL cc_start: 0.8993 (t) cc_final: 0.8451 (p) REVERT: B 979 ASP cc_start: 0.7563 (m-30) cc_final: 0.6970 (m-30) REVERT: C 46 SER cc_start: 0.9077 (m) cc_final: 0.8810 (p) REVERT: C 117 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7018 (pp) REVERT: C 154 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4951 (mp0) REVERT: C 179 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5704 (tp) REVERT: C 186 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5616 (m-80) REVERT: C 265 TYR cc_start: 0.6364 (p90) cc_final: 0.6097 (p90) REVERT: C 306 PHE cc_start: 0.8049 (m-80) cc_final: 0.7472 (m-80) REVERT: C 314 GLN cc_start: 0.8090 (tp40) cc_final: 0.7816 (tp40) REVERT: C 569 ILE cc_start: 0.8419 (mm) cc_final: 0.8015 (mt) REVERT: C 633 TRP cc_start: 0.7924 (p-90) cc_final: 0.7648 (p-90) REVERT: C 913 GLN cc_start: 0.8034 (pt0) cc_final: 0.7821 (pt0) REVERT: C 1023 ASN cc_start: 0.8182 (m-40) cc_final: 0.7883 (m110) REVERT: C 1148 PHE cc_start: 0.5657 (t80) cc_final: 0.4611 (t80) outliers start: 78 outliers final: 21 residues processed: 1027 average time/residue: 0.1778 time to fit residues: 281.3770 Evaluate side-chains 744 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 717 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.0070 chunk 298 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 207 HIS A 360 ASN A 388 ASN A 563 GLN A 658 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 125 ASN B 207 HIS B 211 ASN B 271 GLN B 437 ASN B 544 ASN B 563 GLN B 784 GLN B 856 ASN B 960 ASN B 965 GLN B1011 GLN C 125 ASN C 196 ASN C 271 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 919 ASN C 955 ASN C 957 GLN C 969 ASN C1119 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078880 restraints weight = 68876.115| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.93 r_work: 0.3089 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27758 Z= 0.178 Angle : 0.891 21.591 37936 Z= 0.434 Chirality : 0.052 0.533 4518 Planarity : 0.005 0.070 4731 Dihedral : 11.781 105.829 5559 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 3.80 % Allowed : 12.67 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3254 helix: 0.62 (0.19), residues: 767 sheet: 0.16 (0.19), residues: 676 loop : -1.60 (0.13), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.032 0.002 TYR C 904 PHE 0.037 0.002 PHE A 175 TRP 0.025 0.002 TRP A 436 HIS 0.013 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00389 (27619) covalent geometry : angle 0.81983 (37562) SS BOND : bond 0.00582 ( 43) SS BOND : angle 1.86779 ( 86) hydrogen bonds : bond 0.05079 ( 1083) hydrogen bonds : angle 6.62254 ( 2973) link_ALPHA1-4 : bond 0.01278 ( 10) link_ALPHA1-4 : angle 3.59830 ( 30) link_BETA1-4 : bond 0.00397 ( 29) link_BETA1-4 : angle 1.92226 ( 87) link_BETA1-6 : bond 0.01528 ( 3) link_BETA1-6 : angle 1.69787 ( 9) link_NAG-ASN : bond 0.00652 ( 54) link_NAG-ASN : angle 4.87957 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 717 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8548 (m) cc_final: 0.8132 (p) REVERT: A 80 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.5634 (m-30) REVERT: A 115 GLN cc_start: 0.8270 (mp10) cc_final: 0.8015 (mm-40) REVERT: A 138 ASP cc_start: 0.8629 (t0) cc_final: 0.8004 (p0) REVERT: A 140 PHE cc_start: 0.8277 (p90) cc_final: 0.8054 (p90) REVERT: A 224 GLU cc_start: 0.8154 (mp0) cc_final: 0.7905 (mp0) REVERT: A 319 ARG cc_start: 0.8781 (ptm-80) cc_final: 0.8435 (ptm160) REVERT: A 320 VAL cc_start: 0.9057 (t) cc_final: 0.8534 (m) REVERT: A 340 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8198 (mp0) REVERT: A 374 PHE cc_start: 0.7667 (m-80) cc_final: 0.7422 (m-80) REVERT: A 384 PRO cc_start: 0.8464 (Cg_endo) cc_final: 0.8177 (Cg_exo) REVERT: A 451 TYR cc_start: 0.7292 (m-80) cc_final: 0.6794 (m-80) REVERT: A 571 ASP cc_start: 0.8179 (t0) cc_final: 0.7763 (t0) REVERT: A 586 ASP cc_start: 0.8166 (m-30) cc_final: 0.7920 (m-30) REVERT: A 590 CYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6907 (p) REVERT: A 591 SER cc_start: 0.9011 (t) cc_final: 0.8317 (p) REVERT: A 619 GLU cc_start: 0.8373 (mp0) cc_final: 0.8083 (mp0) REVERT: A 661 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 697 MET cc_start: 0.8623 (ptm) cc_final: 0.8240 (ptm) REVERT: A 737 ASP cc_start: 0.8179 (t0) cc_final: 0.7969 (t0) REVERT: A 763 LEU cc_start: 0.9155 (mt) cc_final: 0.8881 (mp) REVERT: A 764 ASN cc_start: 0.8789 (m-40) cc_final: 0.8486 (m110) REVERT: A 790 LYS cc_start: 0.8878 (mttm) cc_final: 0.8603 (mttm) REVERT: A 957 GLN cc_start: 0.8787 (tt0) cc_final: 0.8568 (tm-30) REVERT: A 985 ASP cc_start: 0.8341 (p0) cc_final: 0.7975 (p0) REVERT: A 986 LYS cc_start: 0.9083 (tptt) cc_final: 0.8818 (tptp) REVERT: A 988 GLU cc_start: 0.8496 (tp30) cc_final: 0.8257 (tp30) REVERT: A 1037 SER cc_start: 0.9226 (t) cc_final: 0.8661 (p) REVERT: A 1119 ASN cc_start: 0.8612 (m-40) cc_final: 0.8395 (m-40) REVERT: B 90 VAL cc_start: 0.8796 (t) cc_final: 0.8572 (p) REVERT: B 96 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6547 (tt0) REVERT: B 121 ASN cc_start: 0.8426 (p0) cc_final: 0.8137 (m-40) REVERT: B 131 CYS cc_start: 0.2273 (OUTLIER) cc_final: 0.0818 (m) REVERT: B 195 LYS cc_start: 0.8727 (tttt) cc_final: 0.8506 (ttpt) REVERT: B 218 GLN cc_start: 0.8644 (tt0) cc_final: 0.8406 (tt0) REVERT: B 271 GLN cc_start: 0.8768 (mt0) cc_final: 0.8506 (mt0) REVERT: B 290 ASP cc_start: 0.7871 (t0) cc_final: 0.7623 (t0) REVERT: B 319 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8647 (ttm-80) REVERT: B 353 TRP cc_start: 0.8321 (p-90) cc_final: 0.8083 (p-90) REVERT: B 396 TYR cc_start: 0.8249 (m-80) cc_final: 0.7953 (m-80) REVERT: B 437 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7956 (m-40) REVERT: B 461 LEU cc_start: 0.9102 (pp) cc_final: 0.8877 (pp) REVERT: B 528 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8730 (ttmm) REVERT: B 580 GLN cc_start: 0.8629 (mt0) cc_final: 0.8423 (mm-40) REVERT: B 581 THR cc_start: 0.8875 (p) cc_final: 0.8441 (t) REVERT: B 651 ILE cc_start: 0.9189 (mt) cc_final: 0.8601 (pt) REVERT: B 696 THR cc_start: 0.9116 (m) cc_final: 0.8795 (p) REVERT: B 697 MET cc_start: 0.8713 (ptm) cc_final: 0.8023 (ptp) REVERT: B 740 MET cc_start: 0.8881 (ttp) cc_final: 0.8483 (ttp) REVERT: B 765 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8283 (ttm110) REVERT: B 790 LYS cc_start: 0.8863 (tttt) cc_final: 0.8607 (ttpt) REVERT: B 808 ASP cc_start: 0.8165 (t0) cc_final: 0.7843 (t70) REVERT: B 824 ASN cc_start: 0.9144 (m-40) cc_final: 0.8751 (m-40) REVERT: B 979 ASP cc_start: 0.8293 (m-30) cc_final: 0.8069 (m-30) REVERT: B 988 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: B 1111 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 1113 GLN cc_start: 0.8717 (mt0) cc_final: 0.8411 (mt0) REVERT: C 65 PHE cc_start: 0.8607 (m-80) cc_final: 0.8406 (m-10) REVERT: C 99 ASN cc_start: 0.8407 (t0) cc_final: 0.8073 (t0) REVERT: C 102 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7839 (mmm160) REVERT: C 238 PHE cc_start: 0.8511 (p90) cc_final: 0.7977 (p90) REVERT: C 271 GLN cc_start: 0.8916 (mt0) cc_final: 0.8490 (mt0) REVERT: C 278 LYS cc_start: 0.8703 (tttt) cc_final: 0.8406 (ttpt) REVERT: C 313 TYR cc_start: 0.8646 (m-80) cc_final: 0.8250 (m-80) REVERT: C 516 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 562 PHE cc_start: 0.8228 (p90) cc_final: 0.7875 (p90) REVERT: C 602 THR cc_start: 0.9279 (m) cc_final: 0.9012 (p) REVERT: C 604 THR cc_start: 0.9016 (m) cc_final: 0.8634 (t) REVERT: C 711 SER cc_start: 0.9218 (t) cc_final: 0.8623 (p) REVERT: C 790 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8607 (ttmm) REVERT: C 900 MET cc_start: 0.9009 (tpp) cc_final: 0.8697 (mtp) REVERT: C 994 ASP cc_start: 0.8610 (t70) cc_final: 0.8339 (t0) REVERT: C 1017 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8301 (tt0) REVERT: C 1041 ASP cc_start: 0.8727 (t0) cc_final: 0.8440 (t0) REVERT: C 1073 LYS cc_start: 0.9081 (mttt) cc_final: 0.8787 (mmmm) REVERT: C 1119 ASN cc_start: 0.8607 (m110) cc_final: 0.8168 (p0) REVERT: C 1148 PHE cc_start: 0.6860 (t80) cc_final: 0.6517 (t80) outliers start: 109 outliers final: 65 residues processed: 776 average time/residue: 0.1659 time to fit residues: 201.9954 Evaluate side-chains 688 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 617 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 42 optimal weight: 5.9990 chunk 85 optimal weight: 0.0070 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 269 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN A 388 ASN A 935 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 564 GLN C 901 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077025 restraints weight = 69140.719| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.89 r_work: 0.3054 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27758 Z= 0.200 Angle : 0.819 18.974 37936 Z= 0.399 Chirality : 0.049 0.392 4518 Planarity : 0.004 0.066 4731 Dihedral : 10.831 103.606 5540 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 4.47 % Allowed : 14.66 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3254 helix: 1.10 (0.19), residues: 771 sheet: 0.03 (0.19), residues: 677 loop : -1.57 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.030 0.002 TYR C 904 PHE 0.036 0.002 PHE A1148 TRP 0.022 0.002 TRP A 436 HIS 0.020 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00446 (27619) covalent geometry : angle 0.76509 (37562) SS BOND : bond 0.00411 ( 43) SS BOND : angle 2.49636 ( 86) hydrogen bonds : bond 0.04707 ( 1083) hydrogen bonds : angle 6.25205 ( 2973) link_ALPHA1-4 : bond 0.01681 ( 10) link_ALPHA1-4 : angle 3.56856 ( 30) link_BETA1-4 : bond 0.00290 ( 29) link_BETA1-4 : angle 1.62250 ( 87) link_BETA1-6 : bond 0.01571 ( 3) link_BETA1-6 : angle 2.19674 ( 9) link_NAG-ASN : bond 0.00467 ( 54) link_NAG-ASN : angle 3.76622 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 660 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7448 (t0) cc_final: 0.7044 (t70) REVERT: A 63 THR cc_start: 0.8585 (m) cc_final: 0.8136 (p) REVERT: A 80 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6220 (m-30) REVERT: A 138 ASP cc_start: 0.8639 (t0) cc_final: 0.7985 (p0) REVERT: A 140 PHE cc_start: 0.8336 (p90) cc_final: 0.8104 (p90) REVERT: A 320 VAL cc_start: 0.9157 (t) cc_final: 0.8640 (m) REVERT: A 340 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8234 (mp0) REVERT: A 374 PHE cc_start: 0.7707 (m-80) cc_final: 0.7443 (m-80) REVERT: A 387 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 396 TYR cc_start: 0.7364 (m-80) cc_final: 0.7021 (m-80) REVERT: A 451 TYR cc_start: 0.7362 (m-80) cc_final: 0.6685 (m-80) REVERT: A 586 ASP cc_start: 0.8178 (m-30) cc_final: 0.7851 (m-30) REVERT: A 591 SER cc_start: 0.9110 (t) cc_final: 0.8622 (p) REVERT: A 619 GLU cc_start: 0.8314 (mp0) cc_final: 0.7979 (mp0) REVERT: A 697 MET cc_start: 0.8602 (ptm) cc_final: 0.8347 (ptm) REVERT: A 737 ASP cc_start: 0.8239 (t0) cc_final: 0.7925 (t0) REVERT: A 763 LEU cc_start: 0.9143 (mt) cc_final: 0.8912 (mp) REVERT: A 764 ASN cc_start: 0.8861 (m-40) cc_final: 0.8543 (m110) REVERT: A 790 LYS cc_start: 0.8843 (mttm) cc_final: 0.8557 (mttm) REVERT: A 957 GLN cc_start: 0.8763 (tt0) cc_final: 0.8558 (tm-30) REVERT: A 968 SER cc_start: 0.9263 (m) cc_final: 0.9056 (t) REVERT: A 1037 SER cc_start: 0.9288 (t) cc_final: 0.8786 (p) REVERT: A 1101 HIS cc_start: 0.7941 (m170) cc_final: 0.7687 (m90) REVERT: A 1137 VAL cc_start: 0.9384 (t) cc_final: 0.9055 (p) REVERT: A 1138 TYR cc_start: 0.8136 (t80) cc_final: 0.7887 (t80) REVERT: B 49 HIS cc_start: 0.8638 (t-90) cc_final: 0.8288 (t-90) REVERT: B 90 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8541 (p) REVERT: B 96 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: B 121 ASN cc_start: 0.8384 (p0) cc_final: 0.7716 (p0) REVERT: B 133 PHE cc_start: 0.7224 (m-80) cc_final: 0.6875 (m-80) REVERT: B 154 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.4319 (mm-30) REVERT: B 195 LYS cc_start: 0.8862 (tttt) cc_final: 0.8639 (ttpt) REVERT: B 218 GLN cc_start: 0.8633 (tt0) cc_final: 0.8405 (tt0) REVERT: B 271 GLN cc_start: 0.8753 (mt0) cc_final: 0.8494 (mt0) REVERT: B 290 ASP cc_start: 0.7965 (t0) cc_final: 0.7695 (t0) REVERT: B 303 LEU cc_start: 0.9396 (tp) cc_final: 0.9058 (tp) REVERT: B 304 LYS cc_start: 0.9290 (mmtp) cc_final: 0.9051 (mmmm) REVERT: B 319 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8476 (ttm-80) REVERT: B 329 PHE cc_start: 0.8550 (m-10) cc_final: 0.8290 (m-80) REVERT: B 353 TRP cc_start: 0.8278 (p-90) cc_final: 0.7731 (p-90) REVERT: B 398 ASP cc_start: 0.8041 (m-30) cc_final: 0.6535 (m-30) REVERT: B 417 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8360 (mmmm) REVERT: B 461 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8320 (pp) REVERT: B 607 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8583 (mt0) REVERT: B 697 MET cc_start: 0.8703 (ptm) cc_final: 0.8320 (ptm) REVERT: B 762 GLN cc_start: 0.8964 (mt0) cc_final: 0.8592 (mt0) REVERT: B 790 LYS cc_start: 0.8915 (tttt) cc_final: 0.8660 (ttpt) REVERT: B 808 ASP cc_start: 0.8173 (t0) cc_final: 0.7654 (t70) REVERT: B 824 ASN cc_start: 0.9141 (m-40) cc_final: 0.8774 (m-40) REVERT: B 918 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 935 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 979 ASP cc_start: 0.8358 (m-30) cc_final: 0.8099 (m-30) REVERT: B 995 ARG cc_start: 0.8817 (mtt-85) cc_final: 0.8376 (mtt-85) REVERT: B 1091 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.7495 (mtp85) REVERT: B 1111 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 1113 GLN cc_start: 0.8764 (mt0) cc_final: 0.8440 (mt0) REVERT: C 41 LYS cc_start: 0.8763 (mttt) cc_final: 0.8308 (mttp) REVERT: C 99 ASN cc_start: 0.8338 (t0) cc_final: 0.8129 (t0) REVERT: C 102 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7879 (mmm160) REVERT: C 117 LEU cc_start: 0.7396 (pp) cc_final: 0.7078 (pp) REVERT: C 125 ASN cc_start: 0.7759 (m-40) cc_final: 0.7262 (m110) REVERT: C 168 PHE cc_start: 0.8204 (t80) cc_final: 0.7901 (t80) REVERT: C 173 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: C 238 PHE cc_start: 0.8605 (p90) cc_final: 0.7981 (p90) REVERT: C 271 GLN cc_start: 0.8901 (mt0) cc_final: 0.8527 (mt0) REVERT: C 278 LYS cc_start: 0.8761 (tttt) cc_final: 0.8496 (ttpt) REVERT: C 287 ASP cc_start: 0.8585 (t0) cc_final: 0.8368 (t0) REVERT: C 313 TYR cc_start: 0.8686 (m-80) cc_final: 0.8359 (m-80) REVERT: C 441 LEU cc_start: 0.8268 (mt) cc_final: 0.7745 (tt) REVERT: C 465 GLU cc_start: 0.8079 (tp30) cc_final: 0.7817 (tp30) REVERT: C 472 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7661 (tt) REVERT: C 473 TYR cc_start: 0.8580 (t80) cc_final: 0.8326 (t80) REVERT: C 558 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8730 (mtmm) REVERT: C 602 THR cc_start: 0.9331 (m) cc_final: 0.9130 (p) REVERT: C 604 THR cc_start: 0.9031 (m) cc_final: 0.8612 (t) REVERT: C 654 GLU cc_start: 0.8471 (tp30) cc_final: 0.8202 (tp30) REVERT: C 702 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 711 SER cc_start: 0.9234 (t) cc_final: 0.8698 (p) REVERT: C 737 ASP cc_start: 0.8378 (t0) cc_final: 0.8147 (t0) REVERT: C 780 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8476 (mm-30) REVERT: C 790 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8642 (ttmm) REVERT: C 994 ASP cc_start: 0.8658 (t70) cc_final: 0.8204 (t0) REVERT: C 1073 LYS cc_start: 0.9068 (mttt) cc_final: 0.8771 (mmtp) REVERT: C 1092 GLU cc_start: 0.8331 (mp0) cc_final: 0.8107 (mp0) REVERT: C 1119 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8175 (p0) REVERT: C 1129 VAL cc_start: 0.9332 (t) cc_final: 0.8913 (p) REVERT: C 1145 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8757 (pp) outliers start: 128 outliers final: 77 residues processed: 742 average time/residue: 0.1655 time to fit residues: 194.3153 Evaluate side-chains 695 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 608 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 29 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 658 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 388 ASN B 437 ASN B 474 GLN B 658 ASN B 784 GLN B1058 HIS C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.076605 restraints weight = 69594.927| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.91 r_work: 0.3043 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27758 Z= 0.191 Angle : 0.795 17.757 37936 Z= 0.383 Chirality : 0.048 0.351 4518 Planarity : 0.004 0.058 4731 Dihedral : 10.271 102.830 5537 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 4.22 % Allowed : 17.03 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3254 helix: 1.31 (0.19), residues: 767 sheet: -0.00 (0.18), residues: 692 loop : -1.64 (0.13), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1019 TYR 0.037 0.002 TYR A 421 PHE 0.038 0.002 PHE A1148 TRP 0.022 0.002 TRP C 436 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00426 (27619) covalent geometry : angle 0.74518 (37562) SS BOND : bond 0.00465 ( 43) SS BOND : angle 2.78115 ( 86) hydrogen bonds : bond 0.04353 ( 1083) hydrogen bonds : angle 6.08033 ( 2973) link_ALPHA1-4 : bond 0.01667 ( 10) link_ALPHA1-4 : angle 3.43792 ( 30) link_BETA1-4 : bond 0.00305 ( 29) link_BETA1-4 : angle 1.51166 ( 87) link_BETA1-6 : bond 0.01558 ( 3) link_BETA1-6 : angle 2.34698 ( 9) link_NAG-ASN : bond 0.00375 ( 54) link_NAG-ASN : angle 3.37170 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 642 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8612 (m) cc_final: 0.8183 (p) REVERT: A 80 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: A 297 SER cc_start: 0.9319 (m) cc_final: 0.8728 (p) REVERT: A 320 VAL cc_start: 0.9093 (t) cc_final: 0.8709 (m) REVERT: A 340 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8165 (tm-30) REVERT: A 374 PHE cc_start: 0.7635 (m-80) cc_final: 0.7340 (m-80) REVERT: A 387 LEU cc_start: 0.9102 (mm) cc_final: 0.8879 (mp) REVERT: A 396 TYR cc_start: 0.7438 (m-80) cc_final: 0.6978 (m-80) REVERT: A 451 TYR cc_start: 0.7350 (m-80) cc_final: 0.6690 (m-80) REVERT: A 586 ASP cc_start: 0.8209 (m-30) cc_final: 0.7821 (m-30) REVERT: A 591 SER cc_start: 0.9079 (t) cc_final: 0.8539 (p) REVERT: A 619 GLU cc_start: 0.8207 (mp0) cc_final: 0.7851 (mp0) REVERT: A 658 ASN cc_start: 0.8531 (t0) cc_final: 0.8283 (t0) REVERT: A 697 MET cc_start: 0.8630 (ptm) cc_final: 0.8233 (ptm) REVERT: A 763 LEU cc_start: 0.9118 (mt) cc_final: 0.8879 (mp) REVERT: A 764 ASN cc_start: 0.8860 (m-40) cc_final: 0.8523 (m110) REVERT: A 823 PHE cc_start: 0.8241 (m-10) cc_final: 0.7969 (m-10) REVERT: A 968 SER cc_start: 0.9268 (m) cc_final: 0.9017 (t) REVERT: A 1037 SER cc_start: 0.9297 (t) cc_final: 0.8858 (p) REVERT: A 1101 HIS cc_start: 0.8035 (m170) cc_final: 0.7814 (m90) REVERT: A 1119 ASN cc_start: 0.8520 (m-40) cc_final: 0.8234 (p0) REVERT: A 1137 VAL cc_start: 0.9436 (t) cc_final: 0.9102 (p) REVERT: B 49 HIS cc_start: 0.8605 (t-90) cc_final: 0.8215 (t-90) REVERT: B 90 VAL cc_start: 0.8757 (t) cc_final: 0.8502 (p) REVERT: B 96 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: B 133 PHE cc_start: 0.7300 (m-80) cc_final: 0.6730 (m-80) REVERT: B 135 PHE cc_start: 0.8155 (m-80) cc_final: 0.7873 (m-80) REVERT: B 271 GLN cc_start: 0.8724 (mt0) cc_final: 0.8490 (mt0) REVERT: B 290 ASP cc_start: 0.8035 (t0) cc_final: 0.7779 (t0) REVERT: B 304 LYS cc_start: 0.9333 (mmtp) cc_final: 0.9105 (mmmm) REVERT: B 319 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.8485 (ttm-80) REVERT: B 329 PHE cc_start: 0.8527 (m-10) cc_final: 0.8278 (m-80) REVERT: B 353 TRP cc_start: 0.8281 (p-90) cc_final: 0.7540 (p-90) REVERT: B 398 ASP cc_start: 0.8026 (m-30) cc_final: 0.6180 (m-30) REVERT: B 399 SER cc_start: 0.8926 (m) cc_final: 0.8711 (p) REVERT: B 516 GLU cc_start: 0.7579 (mp0) cc_final: 0.7242 (mp0) REVERT: B 607 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8567 (mt0) REVERT: B 695 TYR cc_start: 0.8873 (p90) cc_final: 0.8503 (p90) REVERT: B 697 MET cc_start: 0.8719 (ptm) cc_final: 0.8439 (ptm) REVERT: B 762 GLN cc_start: 0.8994 (mt0) cc_final: 0.8593 (mt0) REVERT: B 790 LYS cc_start: 0.8935 (tttt) cc_final: 0.8699 (ttpt) REVERT: B 808 ASP cc_start: 0.8141 (t0) cc_final: 0.7584 (t70) REVERT: B 824 ASN cc_start: 0.9130 (m-40) cc_final: 0.8752 (m-40) REVERT: B 867 ASP cc_start: 0.7976 (t0) cc_final: 0.7649 (t0) REVERT: B 918 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 935 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 979 ASP cc_start: 0.8356 (m-30) cc_final: 0.8088 (m-30) REVERT: B 995 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.8276 (mtt-85) REVERT: B 1111 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 1113 GLN cc_start: 0.8693 (mt0) cc_final: 0.8372 (mt0) REVERT: C 41 LYS cc_start: 0.8752 (mttt) cc_final: 0.8242 (mttp) REVERT: C 102 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7858 (mmm160) REVERT: C 154 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.5659 (mm-30) REVERT: C 173 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8120 (mm110) REVERT: C 271 GLN cc_start: 0.9022 (mt0) cc_final: 0.8667 (mt0) REVERT: C 278 LYS cc_start: 0.8767 (tttt) cc_final: 0.8442 (ttpp) REVERT: C 321 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8999 (mm110) REVERT: C 462 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8829 (mttt) REVERT: C 465 GLU cc_start: 0.8148 (tp30) cc_final: 0.7881 (tp30) REVERT: C 516 GLU cc_start: 0.8028 (pt0) cc_final: 0.7672 (pt0) REVERT: C 604 THR cc_start: 0.9039 (m) cc_final: 0.8600 (t) REVERT: C 613 GLN cc_start: 0.8570 (mt0) cc_final: 0.8308 (mt0) REVERT: C 654 GLU cc_start: 0.8547 (tp30) cc_final: 0.8243 (tp30) REVERT: C 711 SER cc_start: 0.9240 (t) cc_final: 0.8713 (p) REVERT: C 780 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8467 (mm-30) REVERT: C 790 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8661 (ttmm) REVERT: C 819 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8212 (mm-30) REVERT: C 988 GLU cc_start: 0.8359 (tp30) cc_final: 0.8114 (mm-30) REVERT: C 994 ASP cc_start: 0.8644 (t70) cc_final: 0.8113 (t0) REVERT: C 1073 LYS cc_start: 0.9041 (mttt) cc_final: 0.8711 (mmtp) REVERT: C 1092 GLU cc_start: 0.8365 (mp0) cc_final: 0.8129 (mp0) REVERT: C 1119 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8138 (p0) REVERT: C 1129 VAL cc_start: 0.9307 (t) cc_final: 0.8878 (p) REVERT: C 1145 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8784 (pp) outliers start: 121 outliers final: 87 residues processed: 719 average time/residue: 0.1682 time to fit residues: 191.0515 Evaluate side-chains 690 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 597 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 307 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 322 optimal weight: 0.0980 chunk 180 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 318 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 836 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 658 ASN B 784 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.097691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077485 restraints weight = 69270.444| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.91 r_work: 0.3057 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27758 Z= 0.151 Angle : 0.759 16.915 37936 Z= 0.364 Chirality : 0.046 0.333 4518 Planarity : 0.004 0.062 4731 Dihedral : 9.676 101.110 5535 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 4.33 % Allowed : 17.77 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3254 helix: 1.48 (0.19), residues: 768 sheet: 0.03 (0.19), residues: 679 loop : -1.64 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 190 TYR 0.028 0.001 TYR C1138 PHE 0.035 0.002 PHE A1148 TRP 0.023 0.001 TRP A 436 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00339 (27619) covalent geometry : angle 0.71469 (37562) SS BOND : bond 0.00347 ( 43) SS BOND : angle 2.29530 ( 86) hydrogen bonds : bond 0.04096 ( 1083) hydrogen bonds : angle 5.95714 ( 2973) link_ALPHA1-4 : bond 0.01734 ( 10) link_ALPHA1-4 : angle 3.62995 ( 30) link_BETA1-4 : bond 0.00331 ( 29) link_BETA1-4 : angle 1.40722 ( 87) link_BETA1-6 : bond 0.01658 ( 3) link_BETA1-6 : angle 2.46017 ( 9) link_NAG-ASN : bond 0.00329 ( 54) link_NAG-ASN : angle 3.12540 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 637 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.8357 (p0) cc_final: 0.7884 (p0) REVERT: A 297 SER cc_start: 0.9235 (m) cc_final: 0.8711 (p) REVERT: A 320 VAL cc_start: 0.9148 (t) cc_final: 0.8717 (m) REVERT: A 340 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8161 (tm-30) REVERT: A 374 PHE cc_start: 0.7609 (m-80) cc_final: 0.7301 (m-80) REVERT: A 451 TYR cc_start: 0.7273 (m-80) cc_final: 0.6584 (m-80) REVERT: A 586 ASP cc_start: 0.8239 (m-30) cc_final: 0.7830 (m-30) REVERT: A 591 SER cc_start: 0.9097 (t) cc_final: 0.8668 (p) REVERT: A 619 GLU cc_start: 0.8188 (mp0) cc_final: 0.7776 (mp0) REVERT: A 661 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 697 MET cc_start: 0.8591 (ptm) cc_final: 0.8161 (ptm) REVERT: A 763 LEU cc_start: 0.9113 (mt) cc_final: 0.8889 (mp) REVERT: A 764 ASN cc_start: 0.8857 (m-40) cc_final: 0.8518 (m110) REVERT: A 819 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8500 (mt-10) REVERT: A 968 SER cc_start: 0.9269 (m) cc_final: 0.8984 (t) REVERT: A 1029 MET cc_start: 0.8925 (tpp) cc_final: 0.8376 (tpp) REVERT: A 1037 SER cc_start: 0.9301 (t) cc_final: 0.8843 (p) REVERT: A 1101 HIS cc_start: 0.8092 (m90) cc_final: 0.7867 (m90) REVERT: A 1119 ASN cc_start: 0.8555 (m-40) cc_final: 0.8284 (p0) REVERT: A 1137 VAL cc_start: 0.9460 (t) cc_final: 0.9136 (p) REVERT: B 49 HIS cc_start: 0.8608 (t-90) cc_final: 0.8359 (t70) REVERT: B 90 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 96 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: B 101 ILE cc_start: 0.9092 (tp) cc_final: 0.8858 (tp) REVERT: B 121 ASN cc_start: 0.8419 (p0) cc_final: 0.8085 (p0) REVERT: B 125 ASN cc_start: 0.8260 (m110) cc_final: 0.7770 (t0) REVERT: B 129 LYS cc_start: 0.8230 (tptp) cc_final: 0.7748 (tptp) REVERT: B 133 PHE cc_start: 0.7204 (m-80) cc_final: 0.6588 (m-80) REVERT: B 135 PHE cc_start: 0.8136 (m-80) cc_final: 0.7857 (m-80) REVERT: B 153 MET cc_start: 0.7526 (ppp) cc_final: 0.7120 (tmm) REVERT: B 154 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5164 (mp0) REVERT: B 239 GLN cc_start: 0.8263 (tp40) cc_final: 0.7938 (tp40) REVERT: B 271 GLN cc_start: 0.8723 (mt0) cc_final: 0.8464 (mt0) REVERT: B 287 ASP cc_start: 0.8842 (t0) cc_final: 0.8636 (t0) REVERT: B 290 ASP cc_start: 0.8053 (t0) cc_final: 0.7785 (t0) REVERT: B 300 LYS cc_start: 0.9237 (mttm) cc_final: 0.9000 (mttm) REVERT: B 304 LYS cc_start: 0.9335 (mmtp) cc_final: 0.9110 (mmmm) REVERT: B 313 TYR cc_start: 0.8997 (m-80) cc_final: 0.8574 (m-80) REVERT: B 319 ARG cc_start: 0.8799 (ttp-110) cc_final: 0.8529 (ttm-80) REVERT: B 353 TRP cc_start: 0.8303 (p-90) cc_final: 0.7684 (p-90) REVERT: B 391 CYS cc_start: 0.7011 (m) cc_final: 0.5800 (m) REVERT: B 398 ASP cc_start: 0.7995 (m-30) cc_final: 0.6192 (m-30) REVERT: B 399 SER cc_start: 0.8920 (m) cc_final: 0.8446 (t) REVERT: B 516 GLU cc_start: 0.7580 (mp0) cc_final: 0.7265 (mp0) REVERT: B 607 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8535 (mt0) REVERT: B 695 TYR cc_start: 0.8848 (p90) cc_final: 0.8461 (p90) REVERT: B 697 MET cc_start: 0.8679 (ptm) cc_final: 0.8377 (ptm) REVERT: B 736 VAL cc_start: 0.9204 (t) cc_final: 0.8817 (m) REVERT: B 737 ASP cc_start: 0.8136 (t0) cc_final: 0.7819 (t0) REVERT: B 762 GLN cc_start: 0.8954 (mt0) cc_final: 0.8568 (mt0) REVERT: B 790 LYS cc_start: 0.8931 (tttt) cc_final: 0.8713 (ttpt) REVERT: B 808 ASP cc_start: 0.8097 (t0) cc_final: 0.7650 (t70) REVERT: B 819 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8155 (mm-30) REVERT: B 824 ASN cc_start: 0.9113 (m-40) cc_final: 0.8730 (m-40) REVERT: B 935 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 979 ASP cc_start: 0.8367 (m-30) cc_final: 0.8105 (m-30) REVERT: B 995 ARG cc_start: 0.8707 (mtt-85) cc_final: 0.8296 (mtp85) REVERT: B 1072 GLU cc_start: 0.8810 (pm20) cc_final: 0.8579 (pm20) REVERT: B 1111 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 1113 GLN cc_start: 0.8723 (mt0) cc_final: 0.8427 (mt0) REVERT: C 41 LYS cc_start: 0.8795 (mttt) cc_final: 0.8428 (mttp) REVERT: C 102 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7797 (mmm160) REVERT: C 154 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.5577 (mm-30) REVERT: C 168 PHE cc_start: 0.8040 (t80) cc_final: 0.7834 (t80) REVERT: C 173 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8155 (mm110) REVERT: C 226 LEU cc_start: 0.7574 (mp) cc_final: 0.7316 (mt) REVERT: C 238 PHE cc_start: 0.8545 (p90) cc_final: 0.7926 (p90) REVERT: C 271 GLN cc_start: 0.9018 (mt0) cc_final: 0.8567 (mt0) REVERT: C 278 LYS cc_start: 0.8801 (tttt) cc_final: 0.8485 (ttpp) REVERT: C 287 ASP cc_start: 0.8551 (t0) cc_final: 0.8351 (t0) REVERT: C 321 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9032 (mm110) REVERT: C 406 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7830 (mp0) REVERT: C 472 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7816 (tt) REVERT: C 516 GLU cc_start: 0.7861 (pt0) cc_final: 0.7576 (pt0) REVERT: C 583 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7777 (tm-30) REVERT: C 585 LEU cc_start: 0.8926 (mt) cc_final: 0.8625 (mt) REVERT: C 592 PHE cc_start: 0.8688 (p90) cc_final: 0.8255 (p90) REVERT: C 604 THR cc_start: 0.9014 (m) cc_final: 0.8568 (t) REVERT: C 633 TRP cc_start: 0.8238 (p-90) cc_final: 0.7514 (p-90) REVERT: C 654 GLU cc_start: 0.8555 (tp30) cc_final: 0.8239 (tp30) REVERT: C 711 SER cc_start: 0.9211 (t) cc_final: 0.8670 (p) REVERT: C 780 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C 790 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8674 (ttmm) REVERT: C 819 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8108 (mm-30) REVERT: C 988 GLU cc_start: 0.8264 (tp30) cc_final: 0.8057 (mm-30) REVERT: C 994 ASP cc_start: 0.8589 (t70) cc_final: 0.8242 (t0) REVERT: C 1073 LYS cc_start: 0.9051 (mttt) cc_final: 0.8707 (mmtp) REVERT: C 1119 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8191 (p0) REVERT: C 1129 VAL cc_start: 0.9273 (t) cc_final: 0.8852 (p) outliers start: 124 outliers final: 84 residues processed: 715 average time/residue: 0.1756 time to fit residues: 198.1545 Evaluate side-chains 695 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 604 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 92 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 301 optimal weight: 0.2980 chunk 265 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 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 360 ASN A 913 GLN B 388 ASN B 658 ASN B 784 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077355 restraints weight = 69591.258| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.89 r_work: 0.3060 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27758 Z= 0.157 Angle : 0.751 16.346 37936 Z= 0.357 Chirality : 0.046 0.497 4518 Planarity : 0.004 0.063 4731 Dihedral : 9.201 100.622 5533 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 4.33 % Allowed : 18.25 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3254 helix: 1.52 (0.19), residues: 775 sheet: -0.02 (0.18), residues: 702 loop : -1.67 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.040 0.001 TYR A 421 PHE 0.024 0.002 PHE A 592 TRP 0.026 0.001 TRP A 436 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00350 (27619) covalent geometry : angle 0.70982 (37562) SS BOND : bond 0.00381 ( 43) SS BOND : angle 2.18439 ( 86) hydrogen bonds : bond 0.03953 ( 1083) hydrogen bonds : angle 5.83206 ( 2973) link_ALPHA1-4 : bond 0.01754 ( 10) link_ALPHA1-4 : angle 3.66217 ( 30) link_BETA1-4 : bond 0.00334 ( 29) link_BETA1-4 : angle 1.35195 ( 87) link_BETA1-6 : bond 0.01708 ( 3) link_BETA1-6 : angle 2.51002 ( 9) link_NAG-ASN : bond 0.00320 ( 54) link_NAG-ASN : angle 3.00540 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 634 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9238 (mp) cc_final: 0.9023 (mt) REVERT: A 63 THR cc_start: 0.8589 (m) cc_final: 0.8180 (p) REVERT: A 138 ASP cc_start: 0.8454 (t0) cc_final: 0.7718 (p0) REVERT: A 340 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8191 (tm-30) REVERT: A 374 PHE cc_start: 0.7568 (m-80) cc_final: 0.7243 (m-80) REVERT: A 396 TYR cc_start: 0.7342 (m-80) cc_final: 0.7011 (m-80) REVERT: A 451 TYR cc_start: 0.7130 (m-80) cc_final: 0.6502 (m-80) REVERT: A 586 ASP cc_start: 0.8230 (m-30) cc_final: 0.7865 (m-30) REVERT: A 619 GLU cc_start: 0.8145 (mp0) cc_final: 0.7658 (mp0) REVERT: A 763 LEU cc_start: 0.9122 (mt) cc_final: 0.8910 (mp) REVERT: A 764 ASN cc_start: 0.8863 (m-40) cc_final: 0.8518 (m110) REVERT: A 823 PHE cc_start: 0.8314 (m-10) cc_final: 0.8038 (m-10) REVERT: A 904 TYR cc_start: 0.8012 (m-80) cc_final: 0.7781 (m-80) REVERT: A 957 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 968 SER cc_start: 0.9254 (m) cc_final: 0.8975 (t) REVERT: A 1029 MET cc_start: 0.8949 (tpp) cc_final: 0.8397 (tpp) REVERT: A 1037 SER cc_start: 0.9303 (t) cc_final: 0.8844 (p) REVERT: A 1101 HIS cc_start: 0.8115 (m90) cc_final: 0.7905 (m90) REVERT: A 1119 ASN cc_start: 0.8573 (m-40) cc_final: 0.8342 (p0) REVERT: A 1137 VAL cc_start: 0.9464 (t) cc_final: 0.9160 (p) REVERT: B 49 HIS cc_start: 0.8681 (t-90) cc_final: 0.8362 (t-90) REVERT: B 90 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 96 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6254 (tt0) REVERT: B 102 ARG cc_start: 0.7626 (mmp80) cc_final: 0.7411 (mmp80) REVERT: B 121 ASN cc_start: 0.8370 (p0) cc_final: 0.7968 (p0) REVERT: B 129 LYS cc_start: 0.8230 (tptp) cc_final: 0.7766 (tptp) REVERT: B 133 PHE cc_start: 0.7105 (m-80) cc_final: 0.6449 (m-80) REVERT: B 153 MET cc_start: 0.7488 (ppp) cc_final: 0.7258 (tmm) REVERT: B 154 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5134 (mp0) REVERT: B 271 GLN cc_start: 0.8682 (mt0) cc_final: 0.8418 (mt0) REVERT: B 287 ASP cc_start: 0.8354 (t0) cc_final: 0.8152 (t0) REVERT: B 296 LEU cc_start: 0.9325 (tp) cc_final: 0.9119 (tt) REVERT: B 304 LYS cc_start: 0.9344 (mmtp) cc_final: 0.9129 (mmmm) REVERT: B 313 TYR cc_start: 0.8999 (m-80) cc_final: 0.8548 (m-80) REVERT: B 319 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8468 (ttm-80) REVERT: B 353 TRP cc_start: 0.8285 (p-90) cc_final: 0.7794 (p-90) REVERT: B 399 SER cc_start: 0.8905 (m) cc_final: 0.8437 (t) REVERT: B 516 GLU cc_start: 0.7621 (mp0) cc_final: 0.7296 (mp0) REVERT: B 607 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8582 (mt0) REVERT: B 695 TYR cc_start: 0.8863 (p90) cc_final: 0.8524 (p90) REVERT: B 697 MET cc_start: 0.8703 (ptm) cc_final: 0.8499 (ptm) REVERT: B 761 THR cc_start: 0.8755 (m) cc_final: 0.8473 (t) REVERT: B 762 GLN cc_start: 0.8877 (mt0) cc_final: 0.8497 (mt0) REVERT: B 773 GLU cc_start: 0.8409 (tt0) cc_final: 0.8205 (tt0) REVERT: B 790 LYS cc_start: 0.8935 (tttt) cc_final: 0.8721 (ttpt) REVERT: B 808 ASP cc_start: 0.8101 (t0) cc_final: 0.7648 (t70) REVERT: B 824 ASN cc_start: 0.9113 (m-40) cc_final: 0.8737 (m-40) REVERT: B 912 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8368 (p) REVERT: B 935 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 955 ASN cc_start: 0.9036 (m-40) cc_final: 0.8627 (t0) REVERT: B 979 ASP cc_start: 0.8408 (m-30) cc_final: 0.8147 (m-30) REVERT: B 995 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.8275 (mtp85) REVERT: B 1072 GLU cc_start: 0.8784 (pm20) cc_final: 0.8564 (pm20) REVERT: B 1111 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 1113 GLN cc_start: 0.8702 (mt0) cc_final: 0.8407 (mt0) REVERT: C 41 LYS cc_start: 0.8790 (mttt) cc_final: 0.8241 (mttp) REVERT: C 53 ASP cc_start: 0.7818 (t0) cc_final: 0.7603 (t0) REVERT: C 102 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7800 (mmm160) REVERT: C 154 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.5451 (mm-30) REVERT: C 173 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8154 (mm110) REVERT: C 202 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7999 (mtmm) REVERT: C 226 LEU cc_start: 0.7566 (mp) cc_final: 0.7304 (mt) REVERT: C 238 PHE cc_start: 0.8551 (p90) cc_final: 0.7979 (p90) REVERT: C 271 GLN cc_start: 0.8982 (mt0) cc_final: 0.8560 (mt0) REVERT: C 278 LYS cc_start: 0.8852 (tttt) cc_final: 0.8561 (ttpp) REVERT: C 321 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8926 (mm-40) REVERT: C 456 PHE cc_start: 0.8458 (m-10) cc_final: 0.8163 (m-10) REVERT: C 472 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7781 (tt) REVERT: C 516 GLU cc_start: 0.7777 (pt0) cc_final: 0.7481 (pt0) REVERT: C 583 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7757 (tm-30) REVERT: C 585 LEU cc_start: 0.8935 (mt) cc_final: 0.8555 (mt) REVERT: C 592 PHE cc_start: 0.8603 (p90) cc_final: 0.8314 (p90) REVERT: C 604 THR cc_start: 0.8995 (m) cc_final: 0.8550 (t) REVERT: C 633 TRP cc_start: 0.8236 (p-90) cc_final: 0.7553 (p-90) REVERT: C 654 GLU cc_start: 0.8550 (tp30) cc_final: 0.8242 (tp30) REVERT: C 711 SER cc_start: 0.9146 (t) cc_final: 0.8699 (p) REVERT: C 780 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8538 (mm-30) REVERT: C 790 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8668 (ttmm) REVERT: C 819 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8156 (mm-30) REVERT: C 988 GLU cc_start: 0.8262 (tp30) cc_final: 0.8032 (mm-30) REVERT: C 994 ASP cc_start: 0.8635 (t70) cc_final: 0.8347 (t0) REVERT: C 1073 LYS cc_start: 0.9045 (mttt) cc_final: 0.8706 (mmtp) REVERT: C 1119 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8205 (p0) REVERT: C 1129 VAL cc_start: 0.9268 (t) cc_final: 0.8861 (p) outliers start: 124 outliers final: 87 residues processed: 711 average time/residue: 0.1655 time to fit residues: 185.9091 Evaluate side-chains 704 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 608 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 257 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 305 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 658 ASN B 777 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076879 restraints weight = 69612.534| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.87 r_work: 0.3050 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27758 Z= 0.178 Angle : 0.761 16.308 37936 Z= 0.365 Chirality : 0.047 0.470 4518 Planarity : 0.004 0.064 4731 Dihedral : 8.829 100.311 5531 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 4.57 % Allowed : 19.69 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3254 helix: 1.54 (0.19), residues: 774 sheet: 0.00 (0.18), residues: 688 loop : -1.69 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 509 TYR 0.034 0.002 TYR A 904 PHE 0.031 0.002 PHE C 168 TRP 0.026 0.001 TRP A 436 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00401 (27619) covalent geometry : angle 0.72226 (37562) SS BOND : bond 0.00447 ( 43) SS BOND : angle 2.10355 ( 86) hydrogen bonds : bond 0.04008 ( 1083) hydrogen bonds : angle 5.83867 ( 2973) link_ALPHA1-4 : bond 0.01711 ( 10) link_ALPHA1-4 : angle 3.61695 ( 30) link_BETA1-4 : bond 0.00331 ( 29) link_BETA1-4 : angle 1.38250 ( 87) link_BETA1-6 : bond 0.01888 ( 3) link_BETA1-6 : angle 2.51808 ( 9) link_NAG-ASN : bond 0.00344 ( 54) link_NAG-ASN : angle 2.90581 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 611 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9240 (mp) cc_final: 0.9039 (mt) REVERT: A 63 THR cc_start: 0.8576 (m) cc_final: 0.8166 (p) REVERT: A 138 ASP cc_start: 0.8452 (t0) cc_final: 0.7521 (p0) REVERT: A 271 GLN cc_start: 0.8613 (mt0) cc_final: 0.8267 (mt0) REVERT: A 287 ASP cc_start: 0.8724 (t0) cc_final: 0.8463 (t0) REVERT: A 320 VAL cc_start: 0.9247 (t) cc_final: 0.8865 (m) REVERT: A 340 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8222 (tm-30) REVERT: A 374 PHE cc_start: 0.7596 (m-80) cc_final: 0.7296 (m-80) REVERT: A 451 TYR cc_start: 0.7117 (m-80) cc_final: 0.6443 (m-80) REVERT: A 571 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7925 (t0) REVERT: A 586 ASP cc_start: 0.8231 (m-30) cc_final: 0.7839 (m-30) REVERT: A 619 GLU cc_start: 0.8086 (mp0) cc_final: 0.7624 (mp0) REVERT: A 697 MET cc_start: 0.8699 (ptm) cc_final: 0.8383 (ptm) REVERT: A 763 LEU cc_start: 0.9127 (mt) cc_final: 0.8917 (mp) REVERT: A 764 ASN cc_start: 0.8870 (m-40) cc_final: 0.8517 (m110) REVERT: A 814 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8414 (mmmm) REVERT: A 819 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8476 (mt-10) REVERT: A 823 PHE cc_start: 0.8304 (m-10) cc_final: 0.8010 (m-10) REVERT: A 904 TYR cc_start: 0.8084 (m-80) cc_final: 0.7823 (m-80) REVERT: A 957 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 968 SER cc_start: 0.9249 (m) cc_final: 0.8972 (t) REVERT: A 1029 MET cc_start: 0.8967 (tpp) cc_final: 0.8398 (tpp) REVERT: A 1037 SER cc_start: 0.9295 (t) cc_final: 0.8864 (p) REVERT: A 1101 HIS cc_start: 0.8141 (m90) cc_final: 0.7932 (m90) REVERT: A 1119 ASN cc_start: 0.8579 (m-40) cc_final: 0.8336 (p0) REVERT: A 1137 VAL cc_start: 0.9483 (t) cc_final: 0.9194 (p) REVERT: A 1138 TYR cc_start: 0.8325 (t80) cc_final: 0.7845 (t80) REVERT: B 49 HIS cc_start: 0.8673 (t-90) cc_final: 0.8430 (t70) REVERT: B 90 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8455 (p) REVERT: B 96 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6477 (tt0) REVERT: B 129 LYS cc_start: 0.8225 (tptp) cc_final: 0.7733 (tptp) REVERT: B 130 VAL cc_start: 0.7783 (t) cc_final: 0.7086 (t) REVERT: B 133 PHE cc_start: 0.7097 (m-80) cc_final: 0.6440 (m-80) REVERT: B 135 PHE cc_start: 0.8114 (m-80) cc_final: 0.7906 (m-80) REVERT: B 154 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.5469 (mp0) REVERT: B 190 ARG cc_start: 0.8602 (mmm160) cc_final: 0.7671 (mmm160) REVERT: B 271 GLN cc_start: 0.8664 (mt0) cc_final: 0.8407 (mt0) REVERT: B 304 LYS cc_start: 0.9342 (mmtp) cc_final: 0.9122 (mmmm) REVERT: B 313 TYR cc_start: 0.9000 (m-80) cc_final: 0.8573 (m-80) REVERT: B 319 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8433 (ttm-80) REVERT: B 398 ASP cc_start: 0.7939 (m-30) cc_final: 0.7521 (m-30) REVERT: B 399 SER cc_start: 0.8917 (m) cc_final: 0.8463 (t) REVERT: B 417 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8061 (tptm) REVERT: B 516 GLU cc_start: 0.7663 (mp0) cc_final: 0.7345 (mp0) REVERT: B 695 TYR cc_start: 0.8882 (p90) cc_final: 0.8577 (p90) REVERT: B 696 THR cc_start: 0.9114 (m) cc_final: 0.8835 (p) REVERT: B 697 MET cc_start: 0.8709 (ptm) cc_final: 0.8449 (ptm) REVERT: B 761 THR cc_start: 0.8689 (m) cc_final: 0.8355 (t) REVERT: B 762 GLN cc_start: 0.8870 (mt0) cc_final: 0.8476 (mt0) REVERT: B 773 GLU cc_start: 0.8383 (tt0) cc_final: 0.8182 (tt0) REVERT: B 790 LYS cc_start: 0.8930 (tttt) cc_final: 0.8715 (ttpt) REVERT: B 808 ASP cc_start: 0.8108 (t0) cc_final: 0.7632 (t70) REVERT: B 824 ASN cc_start: 0.9106 (m-40) cc_final: 0.8733 (m-40) REVERT: B 858 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8574 (mm) REVERT: B 912 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8384 (p) REVERT: B 935 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 955 ASN cc_start: 0.9060 (m-40) cc_final: 0.8628 (t0) REVERT: B 979 ASP cc_start: 0.8425 (m-30) cc_final: 0.8180 (m-30) REVERT: B 990 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 995 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8249 (mtp85) REVERT: B 1111 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 1113 GLN cc_start: 0.8683 (mt0) cc_final: 0.8388 (mt0) REVERT: C 41 LYS cc_start: 0.8776 (mttt) cc_final: 0.8441 (mttp) REVERT: C 102 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7820 (mmt-90) REVERT: C 153 MET cc_start: 0.6590 (ptm) cc_final: 0.6383 (ptm) REVERT: C 154 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: C 173 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8173 (mm-40) REVERT: C 202 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7971 (mtmm) REVERT: C 226 LEU cc_start: 0.7620 (mp) cc_final: 0.7371 (mt) REVERT: C 238 PHE cc_start: 0.8550 (p90) cc_final: 0.7982 (p90) REVERT: C 271 GLN cc_start: 0.9003 (mt0) cc_final: 0.8590 (mt0) REVERT: C 275 PHE cc_start: 0.8908 (m-80) cc_final: 0.8487 (m-80) REVERT: C 321 GLN cc_start: 0.9309 (mm-40) cc_final: 0.9059 (mm-40) REVERT: C 396 TYR cc_start: 0.8506 (m-80) cc_final: 0.8286 (m-80) REVERT: C 441 LEU cc_start: 0.8458 (mt) cc_final: 0.8002 (tt) REVERT: C 472 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7772 (tt) REVERT: C 516 GLU cc_start: 0.7767 (pt0) cc_final: 0.7449 (pt0) REVERT: C 551 VAL cc_start: 0.9035 (t) cc_final: 0.8809 (m) REVERT: C 558 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8733 (mtmm) REVERT: C 583 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 585 LEU cc_start: 0.8912 (mt) cc_final: 0.8382 (mt) REVERT: C 592 PHE cc_start: 0.8622 (p90) cc_final: 0.8257 (p90) REVERT: C 633 TRP cc_start: 0.8232 (p-90) cc_final: 0.7542 (p-90) REVERT: C 711 SER cc_start: 0.9139 (t) cc_final: 0.8714 (p) REVERT: C 780 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8542 (mm-30) REVERT: C 790 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8684 (ttmm) REVERT: C 819 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8162 (mm-30) REVERT: C 988 GLU cc_start: 0.8220 (tp30) cc_final: 0.7986 (mm-30) REVERT: C 994 ASP cc_start: 0.8642 (t70) cc_final: 0.8345 (t0) REVERT: C 1073 LYS cc_start: 0.9058 (mttt) cc_final: 0.8702 (mmtp) REVERT: C 1119 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8166 (p0) REVERT: C 1129 VAL cc_start: 0.9268 (t) cc_final: 0.8869 (p) REVERT: C 1145 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8748 (pp) outliers start: 131 outliers final: 94 residues processed: 701 average time/residue: 0.1670 time to fit residues: 185.2077 Evaluate side-chains 697 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 591 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 154 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN B 388 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076925 restraints weight = 69938.621| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.88 r_work: 0.3053 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27758 Z= 0.166 Angle : 0.754 15.936 37936 Z= 0.360 Chirality : 0.046 0.426 4518 Planarity : 0.004 0.065 4731 Dihedral : 8.358 98.911 5531 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 4.15 % Allowed : 20.38 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3254 helix: 1.54 (0.19), residues: 775 sheet: -0.00 (0.18), residues: 690 loop : -1.70 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.033 0.002 TYR B 660 PHE 0.021 0.002 PHE A 592 TRP 0.028 0.001 TRP A 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00373 (27619) covalent geometry : angle 0.71724 (37562) SS BOND : bond 0.00403 ( 43) SS BOND : angle 1.93498 ( 86) hydrogen bonds : bond 0.03923 ( 1083) hydrogen bonds : angle 5.79566 ( 2973) link_ALPHA1-4 : bond 0.01722 ( 10) link_ALPHA1-4 : angle 3.71492 ( 30) link_BETA1-4 : bond 0.00317 ( 29) link_BETA1-4 : angle 1.37892 ( 87) link_BETA1-6 : bond 0.02115 ( 3) link_BETA1-6 : angle 2.33507 ( 9) link_NAG-ASN : bond 0.00351 ( 54) link_NAG-ASN : angle 2.83558 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 614 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8593 (m) cc_final: 0.8178 (p) REVERT: A 271 GLN cc_start: 0.8627 (mt0) cc_final: 0.8303 (mt0) REVERT: A 287 ASP cc_start: 0.8739 (t0) cc_final: 0.8496 (t0) REVERT: A 320 VAL cc_start: 0.9258 (t) cc_final: 0.8879 (m) REVERT: A 340 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8228 (tm-30) REVERT: A 374 PHE cc_start: 0.7592 (m-80) cc_final: 0.7306 (m-80) REVERT: A 451 TYR cc_start: 0.7086 (m-80) cc_final: 0.6377 (m-80) REVERT: A 512 VAL cc_start: 0.8014 (t) cc_final: 0.7627 (p) REVERT: A 586 ASP cc_start: 0.8179 (m-30) cc_final: 0.7835 (m-30) REVERT: A 619 GLU cc_start: 0.8031 (mp0) cc_final: 0.7611 (mp0) REVERT: A 697 MET cc_start: 0.8682 (ptm) cc_final: 0.8435 (ptm) REVERT: A 763 LEU cc_start: 0.9134 (mt) cc_final: 0.8934 (mp) REVERT: A 764 ASN cc_start: 0.8871 (m-40) cc_final: 0.8515 (m110) REVERT: A 790 LYS cc_start: 0.8699 (mttm) cc_final: 0.8384 (mttm) REVERT: A 814 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8426 (mmmm) REVERT: A 819 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8456 (mt-10) REVERT: A 823 PHE cc_start: 0.8293 (m-10) cc_final: 0.8000 (m-10) REVERT: A 904 TYR cc_start: 0.8104 (m-80) cc_final: 0.7862 (m-80) REVERT: A 913 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8577 (pt0) REVERT: A 957 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 968 SER cc_start: 0.9251 (m) cc_final: 0.8961 (t) REVERT: A 1019 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.8145 (ttp-170) REVERT: A 1029 MET cc_start: 0.8955 (tpp) cc_final: 0.8435 (tpp) REVERT: A 1101 HIS cc_start: 0.8180 (m90) cc_final: 0.7907 (m90) REVERT: A 1119 ASN cc_start: 0.8600 (m-40) cc_final: 0.8346 (p0) REVERT: A 1137 VAL cc_start: 0.9485 (t) cc_final: 0.9201 (p) REVERT: A 1138 TYR cc_start: 0.8328 (t80) cc_final: 0.7826 (t80) REVERT: B 90 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 96 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6540 (tt0) REVERT: B 125 ASN cc_start: 0.8401 (m110) cc_final: 0.8054 (t0) REVERT: B 129 LYS cc_start: 0.8220 (tptp) cc_final: 0.7696 (tptp) REVERT: B 130 VAL cc_start: 0.7900 (t) cc_final: 0.7192 (t) REVERT: B 133 PHE cc_start: 0.7130 (m-80) cc_final: 0.6450 (m-80) REVERT: B 135 PHE cc_start: 0.8061 (m-80) cc_final: 0.7858 (m-80) REVERT: B 154 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.5521 (mp0) REVERT: B 271 GLN cc_start: 0.8687 (mt0) cc_final: 0.8425 (mt0) REVERT: B 287 ASP cc_start: 0.8208 (t0) cc_final: 0.7645 (t0) REVERT: B 304 LYS cc_start: 0.9348 (mmtp) cc_final: 0.9131 (mmmm) REVERT: B 313 TYR cc_start: 0.8986 (m-80) cc_final: 0.8549 (m-80) REVERT: B 319 ARG cc_start: 0.8755 (ttp-110) cc_final: 0.8476 (ptp-110) REVERT: B 398 ASP cc_start: 0.7978 (m-30) cc_final: 0.7287 (m-30) REVERT: B 399 SER cc_start: 0.8921 (m) cc_final: 0.8454 (t) REVERT: B 417 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8115 (tptm) REVERT: B 516 GLU cc_start: 0.7645 (mp0) cc_final: 0.7339 (mp0) REVERT: B 695 TYR cc_start: 0.8867 (p90) cc_final: 0.8612 (p90) REVERT: B 696 THR cc_start: 0.9114 (m) cc_final: 0.8874 (p) REVERT: B 697 MET cc_start: 0.8704 (ptm) cc_final: 0.8359 (ptp) REVERT: B 740 MET cc_start: 0.8613 (ttp) cc_final: 0.8303 (ttp) REVERT: B 761 THR cc_start: 0.8733 (m) cc_final: 0.8374 (t) REVERT: B 762 GLN cc_start: 0.8859 (mt0) cc_final: 0.8531 (mt0) REVERT: B 790 LYS cc_start: 0.8944 (tttt) cc_final: 0.8733 (ttpt) REVERT: B 808 ASP cc_start: 0.8158 (t0) cc_final: 0.7686 (t70) REVERT: B 819 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 824 ASN cc_start: 0.9083 (m-40) cc_final: 0.8707 (m-40) REVERT: B 858 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8632 (mm) REVERT: B 912 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8396 (p) REVERT: B 935 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 955 ASN cc_start: 0.9068 (m-40) cc_final: 0.8623 (t0) REVERT: B 979 ASP cc_start: 0.8451 (m-30) cc_final: 0.8182 (m-30) REVERT: B 990 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 995 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8382 (mtp85) REVERT: B 1111 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 1113 GLN cc_start: 0.8676 (mt0) cc_final: 0.8382 (mt0) REVERT: C 41 LYS cc_start: 0.8797 (mttt) cc_final: 0.8397 (mttp) REVERT: C 53 ASP cc_start: 0.7791 (t0) cc_final: 0.7522 (t0) REVERT: C 102 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7835 (mmt-90) REVERT: C 154 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: C 173 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8200 (mm-40) REVERT: C 202 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: C 226 LEU cc_start: 0.7631 (mp) cc_final: 0.7380 (mt) REVERT: C 238 PHE cc_start: 0.8548 (p90) cc_final: 0.7984 (p90) REVERT: C 271 GLN cc_start: 0.9000 (mt0) cc_final: 0.8583 (mt0) REVERT: C 275 PHE cc_start: 0.8930 (m-80) cc_final: 0.8530 (m-80) REVERT: C 321 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9053 (mm-40) REVERT: C 396 TYR cc_start: 0.8516 (m-80) cc_final: 0.8306 (m-80) REVERT: C 441 LEU cc_start: 0.8482 (mt) cc_final: 0.8050 (tt) REVERT: C 472 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7615 (tt) REVERT: C 516 GLU cc_start: 0.7684 (pt0) cc_final: 0.7336 (pt0) REVERT: C 551 VAL cc_start: 0.9009 (t) cc_final: 0.8807 (m) REVERT: C 592 PHE cc_start: 0.8544 (p90) cc_final: 0.8152 (p90) REVERT: C 633 TRP cc_start: 0.8236 (p-90) cc_final: 0.7524 (p-90) REVERT: C 711 SER cc_start: 0.9123 (t) cc_final: 0.8715 (p) REVERT: C 780 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8522 (mm-30) REVERT: C 790 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8675 (ttmm) REVERT: C 819 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8152 (mm-30) REVERT: C 868 GLU cc_start: 0.8593 (mp0) cc_final: 0.8270 (mp0) REVERT: C 988 GLU cc_start: 0.8228 (tp30) cc_final: 0.7975 (mm-30) REVERT: C 994 ASP cc_start: 0.8634 (t70) cc_final: 0.8262 (t0) REVERT: C 1073 LYS cc_start: 0.9048 (mttt) cc_final: 0.8691 (mmtp) REVERT: C 1119 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8136 (p0) REVERT: C 1129 VAL cc_start: 0.9242 (t) cc_final: 0.8852 (p) outliers start: 119 outliers final: 99 residues processed: 690 average time/residue: 0.1672 time to fit residues: 183.1632 Evaluate side-chains 706 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 596 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 313 optimal weight: 0.5980 chunk 322 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 152 optimal weight: 0.0050 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 296 optimal weight: 0.0970 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN B 81 ASN B 388 ASN B 658 ASN B 777 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078049 restraints weight = 69761.526| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.88 r_work: 0.3075 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27758 Z= 0.139 Angle : 0.744 15.580 37936 Z= 0.353 Chirality : 0.046 0.397 4518 Planarity : 0.004 0.066 4731 Dihedral : 7.794 96.303 5531 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 3.53 % Allowed : 21.54 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3254 helix: 1.66 (0.19), residues: 772 sheet: 0.03 (0.18), residues: 700 loop : -1.62 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.025 0.001 TYR A 904 PHE 0.026 0.001 PHE A 592 TRP 0.032 0.001 TRP A 436 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00310 (27619) covalent geometry : angle 0.71034 (37562) SS BOND : bond 0.00345 ( 43) SS BOND : angle 1.72448 ( 86) hydrogen bonds : bond 0.03747 ( 1083) hydrogen bonds : angle 5.72792 ( 2973) link_ALPHA1-4 : bond 0.01746 ( 10) link_ALPHA1-4 : angle 3.71135 ( 30) link_BETA1-4 : bond 0.00349 ( 29) link_BETA1-4 : angle 1.32882 ( 87) link_BETA1-6 : bond 0.02291 ( 3) link_BETA1-6 : angle 2.18661 ( 9) link_NAG-ASN : bond 0.00321 ( 54) link_NAG-ASN : angle 2.72134 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 627 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8618 (mm) cc_final: 0.8368 (mm) REVERT: A 271 GLN cc_start: 0.8545 (mt0) cc_final: 0.8242 (mt0) REVERT: A 320 VAL cc_start: 0.9252 (t) cc_final: 0.8801 (m) REVERT: A 340 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8235 (tm-30) REVERT: A 374 PHE cc_start: 0.7467 (m-80) cc_final: 0.7196 (m-80) REVERT: A 451 TYR cc_start: 0.7050 (m-80) cc_final: 0.6331 (m-80) REVERT: A 571 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7793 (t0) REVERT: A 586 ASP cc_start: 0.8156 (m-30) cc_final: 0.7848 (m-30) REVERT: A 619 GLU cc_start: 0.7953 (mp0) cc_final: 0.7613 (mp0) REVERT: A 697 MET cc_start: 0.8696 (ptm) cc_final: 0.8371 (ptm) REVERT: A 763 LEU cc_start: 0.9143 (mt) cc_final: 0.8931 (mp) REVERT: A 764 ASN cc_start: 0.8865 (m-40) cc_final: 0.8505 (m110) REVERT: A 790 LYS cc_start: 0.8695 (mttm) cc_final: 0.8450 (mttp) REVERT: A 814 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8413 (mmmm) REVERT: A 819 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 823 PHE cc_start: 0.8278 (m-10) cc_final: 0.7979 (m-10) REVERT: A 904 TYR cc_start: 0.8113 (m-80) cc_final: 0.7896 (m-80) REVERT: A 957 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 968 SER cc_start: 0.9248 (m) cc_final: 0.8938 (t) REVERT: A 1019 ARG cc_start: 0.8498 (tmm-80) cc_final: 0.7975 (ttp-170) REVERT: A 1029 MET cc_start: 0.8932 (tpp) cc_final: 0.8455 (tpp) REVERT: A 1101 HIS cc_start: 0.8159 (m90) cc_final: 0.7905 (m90) REVERT: A 1107 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8134 (mtt180) REVERT: A 1119 ASN cc_start: 0.8602 (m-40) cc_final: 0.8385 (p0) REVERT: A 1137 VAL cc_start: 0.9478 (t) cc_final: 0.9199 (p) REVERT: A 1138 TYR cc_start: 0.8298 (t80) cc_final: 0.7777 (t80) REVERT: B 81 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7388 (t0) REVERT: B 90 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 96 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: B 129 LYS cc_start: 0.8208 (tptp) cc_final: 0.7680 (tptp) REVERT: B 130 VAL cc_start: 0.7891 (t) cc_final: 0.7226 (t) REVERT: B 153 MET cc_start: 0.7544 (tmm) cc_final: 0.7204 (tmm) REVERT: B 154 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5166 (mp0) REVERT: B 226 LEU cc_start: 0.9022 (tp) cc_final: 0.8784 (tp) REVERT: B 239 GLN cc_start: 0.8362 (tp40) cc_final: 0.7799 (mm-40) REVERT: B 271 GLN cc_start: 0.8657 (mt0) cc_final: 0.8392 (mt0) REVERT: B 287 ASP cc_start: 0.8059 (t0) cc_final: 0.7497 (t0) REVERT: B 304 LYS cc_start: 0.9335 (mmtp) cc_final: 0.9118 (mmmm) REVERT: B 310 LYS cc_start: 0.8985 (tttt) cc_final: 0.8717 (ttpt) REVERT: B 313 TYR cc_start: 0.8940 (m-80) cc_final: 0.8434 (m-80) REVERT: B 319 ARG cc_start: 0.8741 (ttp-110) cc_final: 0.8458 (ptp-110) REVERT: B 353 TRP cc_start: 0.8283 (p-90) cc_final: 0.7611 (p-90) REVERT: B 398 ASP cc_start: 0.7936 (m-30) cc_final: 0.6987 (m-30) REVERT: B 399 SER cc_start: 0.8863 (m) cc_final: 0.8647 (p) REVERT: B 417 LYS cc_start: 0.8332 (mmmm) cc_final: 0.8054 (tptm) REVERT: B 436 TRP cc_start: 0.8002 (p90) cc_final: 0.7475 (p90) REVERT: B 516 GLU cc_start: 0.7581 (mp0) cc_final: 0.7309 (mp0) REVERT: B 695 TYR cc_start: 0.8816 (p90) cc_final: 0.8588 (p90) REVERT: B 696 THR cc_start: 0.9103 (m) cc_final: 0.8840 (p) REVERT: B 697 MET cc_start: 0.8673 (ptm) cc_final: 0.8467 (ptm) REVERT: B 762 GLN cc_start: 0.8805 (mt0) cc_final: 0.8551 (mt0) REVERT: B 773 GLU cc_start: 0.8482 (tt0) cc_final: 0.8202 (tp30) REVERT: B 790 LYS cc_start: 0.8929 (tttt) cc_final: 0.8725 (ttpt) REVERT: B 808 ASP cc_start: 0.8206 (t0) cc_final: 0.7773 (t70) REVERT: B 824 ASN cc_start: 0.9041 (m-40) cc_final: 0.8662 (m-40) REVERT: B 858 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8646 (mm) REVERT: B 904 TYR cc_start: 0.8345 (m-10) cc_final: 0.7999 (m-10) REVERT: B 935 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 955 ASN cc_start: 0.9073 (m-40) cc_final: 0.8620 (t0) REVERT: B 979 ASP cc_start: 0.8460 (m-30) cc_final: 0.8192 (m-30) REVERT: B 990 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 995 ARG cc_start: 0.8676 (mtt-85) cc_final: 0.8387 (mtp85) REVERT: B 1111 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 1113 GLN cc_start: 0.8647 (mt0) cc_final: 0.8362 (mt0) REVERT: C 41 LYS cc_start: 0.8799 (mttt) cc_final: 0.8460 (mttp) REVERT: C 102 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7824 (mmt-90) REVERT: C 153 MET cc_start: 0.6556 (ptm) cc_final: 0.6349 (ptm) REVERT: C 154 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: C 173 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8255 (mm-40) REVERT: C 190 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7917 (mmt90) REVERT: C 202 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7967 (mtmm) REVERT: C 226 LEU cc_start: 0.7642 (mp) cc_final: 0.7323 (mt) REVERT: C 238 PHE cc_start: 0.8518 (p90) cc_final: 0.7955 (p90) REVERT: C 271 GLN cc_start: 0.8985 (mt0) cc_final: 0.8574 (mt0) REVERT: C 275 PHE cc_start: 0.8900 (m-80) cc_final: 0.8538 (m-80) REVERT: C 278 LYS cc_start: 0.8921 (tttt) cc_final: 0.8538 (tttt) REVERT: C 298 GLU cc_start: 0.8788 (tt0) cc_final: 0.8485 (tp30) REVERT: C 321 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9065 (mm-40) REVERT: C 436 TRP cc_start: 0.8036 (p90) cc_final: 0.7819 (p90) REVERT: C 437 ASN cc_start: 0.8454 (t0) cc_final: 0.8162 (m-40) REVERT: C 441 LEU cc_start: 0.8463 (mt) cc_final: 0.8016 (tt) REVERT: C 562 PHE cc_start: 0.8094 (p90) cc_final: 0.7581 (p90) REVERT: C 583 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 585 LEU cc_start: 0.8957 (mt) cc_final: 0.8554 (mt) REVERT: C 633 TRP cc_start: 0.8231 (p-90) cc_final: 0.7506 (p-90) REVERT: C 711 SER cc_start: 0.9084 (t) cc_final: 0.8705 (p) REVERT: C 768 THR cc_start: 0.8983 (m) cc_final: 0.8703 (p) REVERT: C 780 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8531 (mm-30) REVERT: C 790 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8668 (ttmm) REVERT: C 819 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8155 (mm-30) REVERT: C 868 GLU cc_start: 0.8574 (mp0) cc_final: 0.8194 (mp0) REVERT: C 988 GLU cc_start: 0.8200 (tp30) cc_final: 0.7974 (mm-30) REVERT: C 994 ASP cc_start: 0.8578 (t70) cc_final: 0.8186 (t0) REVERT: C 1073 LYS cc_start: 0.9037 (mttt) cc_final: 0.8682 (mmtp) REVERT: C 1111 GLU cc_start: 0.8481 (tt0) cc_final: 0.8205 (pt0) REVERT: C 1119 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8137 (p0) REVERT: C 1129 VAL cc_start: 0.9219 (t) cc_final: 0.8800 (p) outliers start: 101 outliers final: 81 residues processed: 690 average time/residue: 0.1703 time to fit residues: 185.5093 Evaluate side-chains 698 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 607 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 159 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 chunk 296 optimal weight: 0.0970 chunk 140 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 263 optimal weight: 0.0980 chunk 220 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 211 ASN B 388 ASN B 784 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.097086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077236 restraints weight = 69884.876| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.88 r_work: 0.3060 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27758 Z= 0.162 Angle : 0.766 15.653 37936 Z= 0.365 Chirality : 0.046 0.409 4518 Planarity : 0.004 0.064 4731 Dihedral : 7.527 96.078 5531 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 3.63 % Allowed : 22.23 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3254 helix: 1.63 (0.19), residues: 772 sheet: 0.01 (0.18), residues: 700 loop : -1.62 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.026 0.001 TYR A 904 PHE 0.029 0.002 PHE A 592 TRP 0.037 0.002 TRP B 64 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00365 (27619) covalent geometry : angle 0.73216 (37562) SS BOND : bond 0.00439 ( 43) SS BOND : angle 1.92488 ( 86) hydrogen bonds : bond 0.03814 ( 1083) hydrogen bonds : angle 5.77860 ( 2973) link_ALPHA1-4 : bond 0.01842 ( 10) link_ALPHA1-4 : angle 3.78086 ( 30) link_BETA1-4 : bond 0.00309 ( 29) link_BETA1-4 : angle 1.33443 ( 87) link_BETA1-6 : bond 0.01765 ( 3) link_BETA1-6 : angle 1.87425 ( 9) link_NAG-ASN : bond 0.00318 ( 54) link_NAG-ASN : angle 2.70465 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 613 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8591 (m) cc_final: 0.8160 (p) REVERT: A 223 LEU cc_start: 0.8593 (mm) cc_final: 0.8338 (mm) REVERT: A 229 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8429 (pp) REVERT: A 271 GLN cc_start: 0.8558 (mt0) cc_final: 0.8263 (mt0) REVERT: A 287 ASP cc_start: 0.8663 (t0) cc_final: 0.8288 (t0) REVERT: A 340 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8247 (tm-30) REVERT: A 374 PHE cc_start: 0.7495 (m-80) cc_final: 0.7253 (m-80) REVERT: A 451 TYR cc_start: 0.7095 (m-80) cc_final: 0.6324 (m-80) REVERT: A 571 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7936 (t0) REVERT: A 586 ASP cc_start: 0.8167 (m-30) cc_final: 0.7847 (m-30) REVERT: A 619 GLU cc_start: 0.7944 (mp0) cc_final: 0.7609 (mp0) REVERT: A 697 MET cc_start: 0.8706 (ptm) cc_final: 0.8461 (ptm) REVERT: A 745 ASP cc_start: 0.7551 (p0) cc_final: 0.7330 (p0) REVERT: A 763 LEU cc_start: 0.9129 (mt) cc_final: 0.8917 (mp) REVERT: A 764 ASN cc_start: 0.8877 (m-40) cc_final: 0.8515 (m110) REVERT: A 814 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8475 (mmmm) REVERT: A 819 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8433 (mt-10) REVERT: A 823 PHE cc_start: 0.8261 (m-10) cc_final: 0.7958 (m-10) REVERT: A 904 TYR cc_start: 0.8195 (m-80) cc_final: 0.7991 (m-80) REVERT: A 957 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 1019 ARG cc_start: 0.8492 (tmm-80) cc_final: 0.8019 (ttp-170) REVERT: A 1029 MET cc_start: 0.8940 (tpp) cc_final: 0.8457 (tpp) REVERT: A 1101 HIS cc_start: 0.8189 (m90) cc_final: 0.7928 (m90) REVERT: A 1107 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8237 (mtt180) REVERT: A 1119 ASN cc_start: 0.8604 (m-40) cc_final: 0.8367 (p0) REVERT: A 1137 VAL cc_start: 0.9472 (t) cc_final: 0.9207 (p) REVERT: A 1138 TYR cc_start: 0.8345 (t80) cc_final: 0.7820 (t80) REVERT: B 90 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 96 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: B 129 LYS cc_start: 0.8242 (tptp) cc_final: 0.7762 (tptp) REVERT: B 130 VAL cc_start: 0.7857 (t) cc_final: 0.7192 (t) REVERT: B 153 MET cc_start: 0.7585 (tmm) cc_final: 0.7313 (tmm) REVERT: B 154 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5334 (mp0) REVERT: B 226 LEU cc_start: 0.8992 (tp) cc_final: 0.8766 (tp) REVERT: B 239 GLN cc_start: 0.8378 (tp40) cc_final: 0.7758 (mm-40) REVERT: B 271 GLN cc_start: 0.8697 (mt0) cc_final: 0.8444 (mt0) REVERT: B 287 ASP cc_start: 0.8115 (t0) cc_final: 0.7560 (t0) REVERT: B 304 LYS cc_start: 0.9323 (mmtp) cc_final: 0.9099 (mmmm) REVERT: B 309 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 313 TYR cc_start: 0.8921 (m-80) cc_final: 0.8420 (m-80) REVERT: B 319 ARG cc_start: 0.8742 (ttp-110) cc_final: 0.8438 (ptp-110) REVERT: B 353 TRP cc_start: 0.8302 (p-90) cc_final: 0.7631 (p-90) REVERT: B 398 ASP cc_start: 0.7922 (m-30) cc_final: 0.6914 (m-30) REVERT: B 399 SER cc_start: 0.8868 (m) cc_final: 0.8661 (p) REVERT: B 417 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8049 (tptm) REVERT: B 436 TRP cc_start: 0.8035 (p90) cc_final: 0.7521 (p90) REVERT: B 516 GLU cc_start: 0.7593 (mp0) cc_final: 0.7329 (mp0) REVERT: B 695 TYR cc_start: 0.8853 (p90) cc_final: 0.8621 (p90) REVERT: B 696 THR cc_start: 0.9110 (m) cc_final: 0.8838 (p) REVERT: B 710 ASN cc_start: 0.9279 (p0) cc_final: 0.9057 (p0) REVERT: B 762 GLN cc_start: 0.8839 (mt0) cc_final: 0.8578 (mt0) REVERT: B 790 LYS cc_start: 0.8935 (tttt) cc_final: 0.8718 (ttpt) REVERT: B 808 ASP cc_start: 0.8268 (t0) cc_final: 0.7842 (t70) REVERT: B 824 ASN cc_start: 0.9049 (m-40) cc_final: 0.8672 (m-40) REVERT: B 858 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8652 (mm) REVERT: B 904 TYR cc_start: 0.8497 (m-10) cc_final: 0.8025 (m-10) REVERT: B 912 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 935 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 950 ASN cc_start: 0.8843 (t0) cc_final: 0.8598 (t0) REVERT: B 955 ASN cc_start: 0.9081 (m-40) cc_final: 0.8628 (t0) REVERT: B 979 ASP cc_start: 0.8467 (m-30) cc_final: 0.8190 (m-30) REVERT: B 990 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 995 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8309 (mtp85) REVERT: B 1111 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7601 (tm-30) REVERT: B 1113 GLN cc_start: 0.8658 (mt0) cc_final: 0.8358 (mt0) REVERT: C 41 LYS cc_start: 0.8811 (mttt) cc_final: 0.8406 (mttp) REVERT: C 53 ASP cc_start: 0.7764 (t0) cc_final: 0.7542 (t0) REVERT: C 55 PHE cc_start: 0.8815 (m-80) cc_final: 0.8412 (m-80) REVERT: C 153 MET cc_start: 0.6505 (ptm) cc_final: 0.6282 (ptm) REVERT: C 154 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: C 190 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7919 (mmt90) REVERT: C 202 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7966 (mtmm) REVERT: C 226 LEU cc_start: 0.7682 (mp) cc_final: 0.7360 (mt) REVERT: C 238 PHE cc_start: 0.8526 (p90) cc_final: 0.7956 (p90) REVERT: C 271 GLN cc_start: 0.8997 (mt0) cc_final: 0.8506 (mt0) REVERT: C 275 PHE cc_start: 0.8905 (m-80) cc_final: 0.8536 (m-80) REVERT: C 278 LYS cc_start: 0.8911 (tttt) cc_final: 0.8526 (tttt) REVERT: C 321 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9082 (mm-40) REVERT: C 434 ILE cc_start: 0.8636 (mp) cc_final: 0.8206 (tp) REVERT: C 436 TRP cc_start: 0.8037 (p90) cc_final: 0.7778 (p90) REVERT: C 437 ASN cc_start: 0.8497 (t0) cc_final: 0.8197 (m-40) REVERT: C 633 TRP cc_start: 0.8231 (p-90) cc_final: 0.7521 (p-90) REVERT: C 711 SER cc_start: 0.9124 (t) cc_final: 0.8653 (p) REVERT: C 780 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8491 (mm-30) REVERT: C 790 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8656 (ttmm) REVERT: C 819 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8146 (mm-30) REVERT: C 868 GLU cc_start: 0.8562 (mp0) cc_final: 0.8193 (mp0) REVERT: C 988 GLU cc_start: 0.8203 (tp30) cc_final: 0.7945 (mm-30) REVERT: C 994 ASP cc_start: 0.8617 (t70) cc_final: 0.8292 (t0) REVERT: C 1073 LYS cc_start: 0.9027 (mttt) cc_final: 0.8674 (mmtp) REVERT: C 1111 GLU cc_start: 0.8561 (tt0) cc_final: 0.8259 (pt0) REVERT: C 1119 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8173 (p0) REVERT: C 1129 VAL cc_start: 0.9231 (t) cc_final: 0.8818 (p) outliers start: 104 outliers final: 85 residues processed: 681 average time/residue: 0.1738 time to fit residues: 185.2282 Evaluate side-chains 694 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 599 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 56 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN C 87 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.095722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076039 restraints weight = 69568.258| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.84 r_work: 0.3039 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27758 Z= 0.208 Angle : 0.783 15.843 37936 Z= 0.376 Chirality : 0.047 0.420 4518 Planarity : 0.005 0.075 4731 Dihedral : 7.457 95.895 5531 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 3.87 % Allowed : 22.16 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3254 helix: 1.51 (0.19), residues: 776 sheet: 0.00 (0.18), residues: 679 loop : -1.68 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 346 TYR 0.031 0.002 TYR A 904 PHE 0.043 0.002 PHE C 347 TRP 0.029 0.002 TRP A 436 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00467 (27619) covalent geometry : angle 0.74923 (37562) SS BOND : bond 0.00434 ( 43) SS BOND : angle 1.93606 ( 86) hydrogen bonds : bond 0.03988 ( 1083) hydrogen bonds : angle 5.82762 ( 2973) link_ALPHA1-4 : bond 0.01790 ( 10) link_ALPHA1-4 : angle 3.87116 ( 30) link_BETA1-4 : bond 0.00298 ( 29) link_BETA1-4 : angle 1.40780 ( 87) link_BETA1-6 : bond 0.01745 ( 3) link_BETA1-6 : angle 1.77248 ( 9) link_NAG-ASN : bond 0.00343 ( 54) link_NAG-ASN : angle 2.74626 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6392.83 seconds wall clock time: 110 minutes 24.66 seconds (6624.66 seconds total)