Starting phenix.real_space_refine on Fri Mar 6 04:06:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7to4_26029/03_2026/7to4_26029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to4_26029/03_2026/7to4_26029.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7to4_26029/03_2026/7to4_26029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to4_26029/03_2026/7to4_26029.map" model { file = "/net/cci-nas-00/data/ceres_data/7to4_26029/03_2026/7to4_26029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to4_26029/03_2026/7to4_26029.cif" } 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17613 2.51 5 N 4473 2.21 5 O 5466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 195 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27672 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8737 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 4 Chain: "B" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "C" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 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: 7.38, per 1000 atoms: 0.27 Number of scatterers: 27672 At special positions: 0 Unit cell: (148.57, 138.61, 220.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5466 8.00 N 4473 7.00 C 17613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.06 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 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 J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG O 2 " - " MAN O 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG W 2 " - " MAN W 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1158 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1158 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " 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 B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6298 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 27.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.557A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.597A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.133A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.557A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.483A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.213A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.697A pdb=" N ALA A 845 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.751A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.519A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.604A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.678A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.652A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.805A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.071A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.161A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.600A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.049A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.105A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 4.207A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.704A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.708A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.554A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.178A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.867A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1161 removed outlier: 3.923A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.865A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.754A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.090A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.393A 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 619 through 624 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.955A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 756 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.102A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.266A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.601A pdb=" N ALA C 846 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.584A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.566A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.039A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.539A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.116A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.599A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.509A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 removed outlier: 4.139A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.981A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.735A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.571A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.735A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.663A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 144 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.992A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.047A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.289A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.887A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.596A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.572A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.669A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.961A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 158 through 160 removed outlier: 8.048A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 12.662A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.840A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE B 144 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.405A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.108A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.934A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.415A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.934A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.890A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.418A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.752A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.809A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.199A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.853A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE C 144 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.891A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.197A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.603A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.330A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.330A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.204A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.787A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 2982 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: 6.95 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4409 1.29 - 1.43: 7540 1.43 - 1.56: 16190 1.56 - 1.70: 2 1.70 - 1.83: 150 Bond restraints: 28291 Sorted by residual: bond pdb=" CA LEU C 118 " pdb=" C LEU C 118 " ideal model delta sigma weight residual 1.522 1.620 -0.097 1.18e-02 7.18e+03 6.81e+01 bond pdb=" C ARG A 983 " pdb=" O ARG A 983 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.11e-02 8.12e+03 5.10e+01 bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.22e-02 6.72e+03 2.57e+01 bond pdb=" C ARG A1019 " pdb=" O ARG A1019 " ideal model delta sigma weight residual 1.237 1.178 0.059 1.16e-02 7.43e+03 2.57e+01 bond pdb=" C ARG C1019 " pdb=" O ARG C1019 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.22e-02 6.72e+03 2.42e+01 ... (remaining 28286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 31152 2.43 - 4.86: 6716 4.86 - 7.29: 555 7.29 - 9.72: 34 9.72 - 12.15: 9 Bond angle restraints: 38466 Sorted by residual: angle pdb=" N ASN C 164 " pdb=" CA ASN C 164 " pdb=" C ASN C 164 " ideal model delta sigma weight residual 110.97 123.12 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.03 102.31 8.72 1.11e+00 8.12e-01 6.18e+01 angle pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" C TYR A 421 " ideal model delta sigma weight residual 113.50 122.46 -8.96 1.23e+00 6.61e-01 5.31e+01 angle pdb=" CA ASP B 389 " pdb=" CB ASP B 389 " pdb=" CG ASP B 389 " ideal model delta sigma weight residual 112.60 119.79 -7.19 1.00e+00 1.00e+00 5.16e+01 angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 109.30 118.64 -9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 17256 25.33 - 50.65: 709 50.65 - 75.98: 145 75.98 - 101.31: 43 101.31 - 126.64: 43 Dihedral angle restraints: 18196 sinusoidal: 8414 harmonic: 9782 Sorted by residual: dihedral pdb=" C ASN C 122 " pdb=" N ASN C 122 " pdb=" CA ASN C 122 " pdb=" CB ASN C 122 " ideal model delta harmonic sigma weight residual -122.60 -138.91 16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" C CYS C1126 " pdb=" N CYS C1126 " pdb=" CA CYS C1126 " pdb=" CB CYS C1126 " ideal model delta harmonic sigma weight residual -122.60 -137.29 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -36.03 -49.97 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 18193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.320: 4583 0.320 - 0.639: 37 0.639 - 0.959: 7 0.959 - 1.279: 3 1.279 - 1.598: 5 Chirality restraints: 4635 Sorted by residual: chirality pdb=" C1 MAN Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 MAN Z 3 " pdb=" O5 MAN Z 3 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 MAN f 3 " pdb=" O4 NAG f 2 " pdb=" C2 MAN f 3 " pdb=" O5 MAN f 3 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.19 2.00e-02 2.50e+03 9.34e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 4632 not shown) Planarity restraints: 4881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.103 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C 234 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.256 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 104 " -0.144 2.00e-02 2.50e+03 7.54e-02 1.42e+02 pdb=" CG TRP A 104 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 104 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 104 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP A 104 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 104 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 104 " -0.091 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 104 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 104 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.100 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A1074 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.160 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.125 2.00e-02 2.50e+03 ... (remaining 4878 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 81 2.59 - 3.17: 22407 3.17 - 3.74: 41775 3.74 - 4.32: 58970 4.32 - 4.90: 94396 Nonbonded interactions: 217629 Sorted by model distance: nonbonded pdb=" O ASN B 17 " pdb=" OD1 ASN B 17 " model vdw 2.009 3.040 nonbonded pdb=" O ASN C 17 " pdb=" OD1 ASN C 17 " model vdw 2.138 3.040 nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 2 " model vdw 2.210 3.040 nonbonded pdb=" N GLN C 836 " pdb=" OE1 GLN C 836 " model vdw 2.211 3.120 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.251 3.120 ... (remaining 217624 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 1307) selection = (chain 'B' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1307)) selection = (chain 'C' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'V' selection = chain 'X' selection = chain 'a' } ncs_group { reference = (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 'M' and resid 1 through 2) selection = (chain 'O' 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 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.590 Find NCS groups from input model: 0.880 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.097 28437 Z= 0.834 Angle : 2.080 50.622 38859 Z= 1.269 Chirality : 0.129 1.598 4635 Planarity : 0.013 0.093 4827 Dihedral : 16.215 126.636 11763 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.19 % Favored : 92.03 % Rotamer: Outliers : 2.60 % Allowed : 5.77 % Favored : 91.63 % Cbeta Deviations : 0.64 % 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: -2.22 (0.13), residues: 3324 helix: -1.76 (0.15), residues: 775 sheet: 0.03 (0.21), residues: 533 loop : -1.85 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 493 TYR 0.120 0.021 TYR B 660 PHE 0.097 0.016 PHE B 898 TRP 0.144 0.026 TRP A 104 HIS 0.022 0.007 HIS A1159 Details of bonding type rmsd covalent geometry : bond 0.01472 (28291) covalent geometry : angle 1.89904 (38466) SS BOND : bond 0.01337 ( 45) SS BOND : angle 2.61879 ( 90) hydrogen bonds : bond 0.17076 ( 1074) hydrogen bonds : angle 8.55754 ( 2982) link_ALPHA1-4 : bond 0.02641 ( 15) link_ALPHA1-4 : angle 4.64069 ( 45) link_BETA1-4 : bond 0.01968 ( 29) link_BETA1-4 : angle 3.61699 ( 87) link_BETA1-6 : bond 0.01663 ( 3) link_BETA1-6 : angle 2.43629 ( 9) link_NAG-ASN : bond 0.01661 ( 54) link_NAG-ASN : angle 12.81470 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 747 time to evaluate : 0.857 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 26 PRO cc_start: 0.7665 (Cg_endo) cc_final: 0.7386 (Cg_exo) REVERT: A 52 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 62 VAL cc_start: 0.8763 (m) cc_final: 0.8539 (p) REVERT: A 116 SER cc_start: 0.8853 (m) cc_final: 0.8576 (m) REVERT: A 120 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 190 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7728 (mmm-85) REVERT: A 197 ILE cc_start: 0.8709 (mm) cc_final: 0.8508 (mm) REVERT: A 224 GLU cc_start: 0.8442 (mp0) cc_final: 0.8188 (mp0) REVERT: A 228 ASP cc_start: 0.7630 (p0) cc_final: 0.7416 (p0) REVERT: A 309 GLU cc_start: 0.8510 (mp0) cc_final: 0.8237 (mp0) REVERT: A 319 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (tpt170) REVERT: A 338 PHE cc_start: 0.7831 (m-80) cc_final: 0.7601 (p90) REVERT: A 424 LYS cc_start: 0.5081 (tptt) cc_final: 0.4568 (tttm) REVERT: A 541 PHE cc_start: 0.6328 (p90) cc_final: 0.5759 (p90) REVERT: A 565 PHE cc_start: 0.7774 (p90) cc_final: 0.7545 (p90) REVERT: A 588 THR cc_start: 0.9018 (m) cc_final: 0.8792 (t) REVERT: A 740 MET cc_start: 0.9044 (tpt) cc_final: 0.8739 (tpp) REVERT: A 773 GLU cc_start: 0.8340 (tt0) cc_final: 0.8023 (tt0) REVERT: A 780 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 811 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7237 (tmtt) REVERT: A 814 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7699 (mmmt) REVERT: A 819 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 820 ASP cc_start: 0.8739 (t70) cc_final: 0.8478 (m-30) REVERT: A 848 ASP cc_start: 0.8429 (t0) cc_final: 0.7573 (p0) REVERT: A 849 LEU cc_start: 0.8750 (mt) cc_final: 0.8329 (mm) REVERT: A 854 LYS cc_start: 0.9288 (tttt) cc_final: 0.9033 (tttt) REVERT: A 856 LYS cc_start: 0.9159 (mptt) cc_final: 0.8888 (mptt) REVERT: A 921 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8484 (mtpp) REVERT: A 925 ASN cc_start: 0.8795 (m110) cc_final: 0.8579 (m-40) REVERT: A 935 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: A 936 ASP cc_start: 0.8845 (m-30) cc_final: 0.8512 (m-30) REVERT: A 950 ASP cc_start: 0.8464 (p0) cc_final: 0.8112 (p0) REVERT: A 964 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8582 (mtpp) REVERT: A 975 SER cc_start: 0.8758 (p) cc_final: 0.8505 (p) REVERT: A 981 PHE cc_start: 0.7738 (m-80) cc_final: 0.6627 (m-80) REVERT: A 1005 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8101 (mm-40) REVERT: A 1019 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8064 (ttp-110) REVERT: A 1072 GLU cc_start: 0.8837 (pm20) cc_final: 0.8355 (pm20) REVERT: A 1073 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8461 (mtpp) REVERT: A 1107 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7339 (mtt-85) REVERT: B 41 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8410 (mmmm) REVERT: B 92 PHE cc_start: 0.8691 (t80) cc_final: 0.8304 (t80) REVERT: B 133 PHE cc_start: 0.7069 (m-80) cc_final: 0.6564 (m-10) REVERT: B 196 ASN cc_start: 0.7978 (t0) cc_final: 0.7685 (t0) REVERT: B 197 ILE cc_start: 0.9020 (tp) cc_final: 0.8708 (pt) REVERT: B 200 TYR cc_start: 0.7650 (m-80) cc_final: 0.7008 (m-80) REVERT: B 202 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8289 (mmmt) REVERT: B 203 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 204 TYR cc_start: 0.8984 (m-80) cc_final: 0.8604 (m-80) REVERT: B 210 ILE cc_start: 0.8702 (tp) cc_final: 0.8471 (tt) REVERT: B 275 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 323 THR cc_start: 0.8705 (t) cc_final: 0.8251 (p) REVERT: B 388 ASN cc_start: 0.8346 (t0) cc_final: 0.8135 (t0) REVERT: B 422 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.6997 (p0) REVERT: B 607 GLN cc_start: 0.8696 (tt0) cc_final: 0.8489 (tp40) REVERT: B 643 PHE cc_start: 0.8555 (t80) cc_final: 0.8262 (t80) REVERT: B 646 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7597 (ttt90) REVERT: B 654 GLU cc_start: 0.8529 (tp30) cc_final: 0.8325 (tp30) REVERT: B 675 GLN cc_start: 0.7695 (pp30) cc_final: 0.7429 (pp30) REVERT: B 751 ASN cc_start: 0.8769 (m110) cc_final: 0.8483 (m110) REVERT: B 755 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: B 765 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8015 (ttm-80) REVERT: B 780 GLU cc_start: 0.8653 (tp30) cc_final: 0.8253 (tp30) REVERT: B 814 LYS cc_start: 0.8550 (mptt) cc_final: 0.8201 (mmmt) REVERT: B 900 MET cc_start: 0.8739 (tpp) cc_final: 0.8381 (mtp) REVERT: B 964 LYS cc_start: 0.9297 (tppt) cc_final: 0.9016 (mmmm) REVERT: B 994 ASP cc_start: 0.8474 (t0) cc_final: 0.8196 (t0) REVERT: B 1005 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8517 (tp40) REVERT: B 1041 ASP cc_start: 0.8538 (t0) cc_final: 0.8074 (t0) REVERT: C 34 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (mtp85) REVERT: C 79 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5890 (m-80) REVERT: C 102 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6762 (mtp180) REVERT: C 154 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: C 218 GLN cc_start: 0.8246 (tt0) cc_final: 0.7989 (tt0) REVERT: C 224 GLU cc_start: 0.8478 (mp0) cc_final: 0.8123 (mp0) REVERT: C 320 VAL cc_start: 0.8948 (t) cc_final: 0.8451 (m) REVERT: C 332 ILE cc_start: 0.8499 (tp) cc_final: 0.8273 (tp) REVERT: C 360 ASN cc_start: 0.8931 (t0) cc_final: 0.8643 (t0) REVERT: C 365 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 377 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 456 PHE cc_start: 0.7416 (m-80) cc_final: 0.7193 (m-10) REVERT: C 547 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8594 (mmmm) REVERT: C 559 PHE cc_start: 0.8330 (m-10) cc_final: 0.7982 (m-10) REVERT: C 564 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8209 (tp40) REVERT: C 565 PHE cc_start: 0.8909 (m-80) cc_final: 0.8677 (m-10) REVERT: C 568 ASP cc_start: 0.7860 (t0) cc_final: 0.7405 (t0) REVERT: C 571 ASP cc_start: 0.7858 (t0) cc_final: 0.7427 (t0) REVERT: C 577 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8517 (ttm170) REVERT: C 584 ILE cc_start: 0.8900 (mm) cc_final: 0.8414 (mm) REVERT: C 610 VAL cc_start: 0.9252 (t) cc_final: 0.8937 (m) REVERT: C 613 GLN cc_start: 0.7975 (mt0) cc_final: 0.7617 (mt0) REVERT: C 661 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 765 ARG cc_start: 0.8454 (ptp-110) cc_final: 0.8207 (mtm110) REVERT: C 780 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 849 LEU cc_start: 0.8779 (mt) cc_final: 0.8553 (tp) REVERT: C 854 LYS cc_start: 0.9183 (tptp) cc_final: 0.8969 (tptp) REVERT: C 855 PHE cc_start: 0.8500 (m-10) cc_final: 0.8056 (m-80) REVERT: C 935 GLN cc_start: 0.8996 (tt0) cc_final: 0.8637 (tt0) REVERT: C 950 ASP cc_start: 0.8373 (p0) cc_final: 0.7826 (p0) REVERT: C 954 HIS cc_start: 0.8222 (m-70) cc_final: 0.8002 (m170) REVERT: C 957 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 991 VAL cc_start: 0.9436 (t) cc_final: 0.9209 (t) REVERT: C 1019 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (ttt-90) outliers start: 76 outliers final: 12 residues processed: 793 average time/residue: 0.2026 time to fit residues: 243.5296 Evaluate side-chains 623 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 596 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 314 GLN A 417 ASN A 481 ASN A 536 ASN A 658 ASN A 901 GLN A 925 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 751 ASN B 935 GLN B 965 GLN B1023 ASN B1119 ASN C 146 HIS C 183 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 544 ASN C 564 GLN C 675 GLN C 762 GLN C 907 ASN C 913 GLN C 953 ASN C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.077566 restraints weight = 76991.147| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.03 r_work: 0.3099 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28437 Z= 0.174 Angle : 0.889 17.553 38859 Z= 0.431 Chirality : 0.053 0.646 4635 Planarity : 0.005 0.054 4827 Dihedral : 12.690 111.153 5744 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 2.63 % Allowed : 11.62 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3324 helix: 0.46 (0.18), residues: 780 sheet: -0.09 (0.19), residues: 606 loop : -1.43 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 190 TYR 0.036 0.002 TYR C 636 PHE 0.046 0.002 PHE A 133 TRP 0.016 0.002 TRP C 353 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00373 (28291) covalent geometry : angle 0.81966 (38466) SS BOND : bond 0.00663 ( 45) SS BOND : angle 1.87266 ( 90) hydrogen bonds : bond 0.05005 ( 1074) hydrogen bonds : angle 6.22860 ( 2982) link_ALPHA1-4 : bond 0.01495 ( 15) link_ALPHA1-4 : angle 2.95514 ( 45) link_BETA1-4 : bond 0.00432 ( 29) link_BETA1-4 : angle 1.99894 ( 87) link_BETA1-6 : bond 0.01614 ( 3) link_BETA1-6 : angle 2.12372 ( 9) link_NAG-ASN : bond 0.00601 ( 54) link_NAG-ASN : angle 4.80712 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 622 time to evaluate : 1.079 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 26 PRO cc_start: 0.7460 (Cg_endo) cc_final: 0.7122 (Cg_exo) REVERT: A 41 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8575 (mmmm) REVERT: A 52 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 62 VAL cc_start: 0.8785 (m) cc_final: 0.8535 (p) REVERT: A 111 ASP cc_start: 0.8167 (p0) cc_final: 0.7405 (t70) REVERT: A 190 ARG cc_start: 0.8456 (mmm160) cc_final: 0.7916 (mmm-85) REVERT: A 195 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8289 (ttpt) REVERT: A 224 GLU cc_start: 0.8412 (mp0) cc_final: 0.8188 (mp0) REVERT: A 228 ASP cc_start: 0.7928 (p0) cc_final: 0.7696 (p0) REVERT: A 287 ASP cc_start: 0.8642 (t0) cc_final: 0.8355 (t0) REVERT: A 306 PHE cc_start: 0.8325 (m-10) cc_final: 0.7859 (m-10) REVERT: A 406 GLU cc_start: 0.0906 (OUTLIER) cc_final: 0.0630 (mp0) REVERT: A 565 PHE cc_start: 0.7795 (p90) cc_final: 0.7564 (p90) REVERT: A 588 THR cc_start: 0.9015 (m) cc_final: 0.8768 (t) REVERT: A 607 GLN cc_start: 0.8299 (mp10) cc_final: 0.8097 (mp10) REVERT: A 658 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.8019 (t0) REVERT: A 660 TYR cc_start: 0.8701 (m-80) cc_final: 0.8336 (m-80) REVERT: A 740 MET cc_start: 0.9163 (tpt) cc_final: 0.8840 (tpp) REVERT: A 752 LEU cc_start: 0.9399 (mm) cc_final: 0.9188 (mp) REVERT: A 773 GLU cc_start: 0.8736 (tt0) cc_final: 0.8390 (tt0) REVERT: A 780 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8477 (mm-30) REVERT: A 819 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 823 PHE cc_start: 0.8055 (m-80) cc_final: 0.7515 (t80) REVERT: A 848 ASP cc_start: 0.8463 (t0) cc_final: 0.7726 (p0) REVERT: A 849 LEU cc_start: 0.8710 (mt) cc_final: 0.8369 (mm) REVERT: A 851 CYS cc_start: 0.8313 (t) cc_final: 0.8058 (t) REVERT: A 854 LYS cc_start: 0.9441 (tttt) cc_final: 0.9207 (tttt) REVERT: A 856 LYS cc_start: 0.9310 (mptt) cc_final: 0.9014 (mptt) REVERT: A 921 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8711 (mtmm) REVERT: A 935 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: A 936 ASP cc_start: 0.8799 (m-30) cc_final: 0.8483 (m-30) REVERT: A 950 ASP cc_start: 0.8425 (p0) cc_final: 0.8042 (p0) REVERT: A 1019 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: A 1072 GLU cc_start: 0.8806 (pm20) cc_final: 0.8495 (pm20) REVERT: A 1148 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6058 (t80) REVERT: B 40 ASP cc_start: 0.8791 (t0) cc_final: 0.8588 (t70) REVERT: B 41 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8439 (mmmm) REVERT: B 52 GLN cc_start: 0.8723 (tp40) cc_final: 0.8293 (tp40) REVERT: B 65 PHE cc_start: 0.8472 (m-10) cc_final: 0.8191 (m-10) REVERT: B 200 TYR cc_start: 0.8046 (m-80) cc_final: 0.7759 (m-80) REVERT: B 202 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8694 (mmtm) REVERT: B 237 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8095 (ptt90) REVERT: B 293 LEU cc_start: 0.9130 (tp) cc_final: 0.8824 (tt) REVERT: B 297 SER cc_start: 0.9270 (m) cc_final: 0.8841 (p) REVERT: B 305 SER cc_start: 0.9150 (t) cc_final: 0.8942 (t) REVERT: B 388 ASN cc_start: 0.8373 (t0) cc_final: 0.8071 (t0) REVERT: B 518 LEU cc_start: 0.9229 (mm) cc_final: 0.8925 (tp) REVERT: B 571 ASP cc_start: 0.8821 (t0) cc_final: 0.8206 (t0) REVERT: B 654 GLU cc_start: 0.8719 (tp30) cc_final: 0.8479 (tp30) REVERT: B 661 GLU cc_start: 0.8476 (pm20) cc_final: 0.8180 (pm20) REVERT: B 675 GLN cc_start: 0.7634 (pp30) cc_final: 0.7414 (pp30) REVERT: B 751 ASN cc_start: 0.8909 (m-40) cc_final: 0.8582 (m-40) REVERT: B 755 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: B 868 GLU cc_start: 0.8502 (mp0) cc_final: 0.8231 (mp0) REVERT: B 900 MET cc_start: 0.8838 (tpp) cc_final: 0.8616 (mtp) REVERT: B 936 ASP cc_start: 0.8427 (m-30) cc_final: 0.8226 (m-30) REVERT: B 983 ARG cc_start: 0.8505 (mpp80) cc_final: 0.8159 (mpp80) REVERT: B 1005 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8600 (tp40) REVERT: B 1010 GLN cc_start: 0.8864 (mt0) cc_final: 0.8536 (mm-40) REVERT: C 81 ASN cc_start: 0.8807 (m-40) cc_final: 0.8376 (m-40) REVERT: C 114 THR cc_start: 0.8325 (t) cc_final: 0.8022 (m) REVERT: C 133 PHE cc_start: 0.7596 (m-80) cc_final: 0.7377 (m-80) REVERT: C 154 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: C 224 GLU cc_start: 0.8504 (mp0) cc_final: 0.8022 (mp0) REVERT: C 242 LEU cc_start: 0.8480 (mm) cc_final: 0.7950 (mm) REVERT: C 360 ASN cc_start: 0.9029 (t0) cc_final: 0.8501 (t0) REVERT: C 377 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.7020 (t80) REVERT: C 547 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8736 (mtpp) REVERT: C 564 GLN cc_start: 0.8848 (tp40) cc_final: 0.8608 (tp40) REVERT: C 568 ASP cc_start: 0.7813 (t0) cc_final: 0.7601 (t0) REVERT: C 571 ASP cc_start: 0.8110 (t0) cc_final: 0.7856 (t0) REVERT: C 610 VAL cc_start: 0.9290 (t) cc_final: 0.9014 (m) REVERT: C 613 GLN cc_start: 0.7897 (mt0) cc_final: 0.7675 (mt0) REVERT: C 646 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8991 (tpp80) REVERT: C 661 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7813 (tm-30) REVERT: C 675 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7733 (pp30) REVERT: C 759 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7504 (t80) REVERT: C 773 GLU cc_start: 0.8673 (tt0) cc_final: 0.8071 (tm-30) REVERT: C 780 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8419 (mm-30) REVERT: C 855 PHE cc_start: 0.8792 (m-10) cc_final: 0.8525 (m-80) REVERT: C 950 ASP cc_start: 0.8144 (p0) cc_final: 0.7827 (p0) REVERT: C 953 ASN cc_start: 0.8779 (m110) cc_final: 0.8458 (m-40) REVERT: C 957 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 979 ASP cc_start: 0.8866 (t0) cc_final: 0.8626 (t0) REVERT: C 1144 GLU cc_start: 0.8518 (mp0) cc_final: 0.8297 (mp0) outliers start: 77 outliers final: 40 residues processed: 654 average time/residue: 0.1908 time to fit residues: 194.6945 Evaluate side-chains 588 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 539 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 307 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 957 GLN A1002 GLN B 125 ASN B 207 HIS B 784 GLN C 183 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075423 restraints weight = 77374.539| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.07 r_work: 0.3050 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 28437 Z= 0.227 Angle : 0.844 17.527 38859 Z= 0.404 Chirality : 0.051 0.585 4635 Planarity : 0.005 0.063 4827 Dihedral : 11.635 111.400 5707 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 3.18 % Allowed : 13.32 % Favored : 83.50 % 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: -0.84 (0.14), residues: 3324 helix: 0.94 (0.19), residues: 779 sheet: -0.14 (0.18), residues: 663 loop : -1.41 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.034 0.002 TYR C 636 PHE 0.030 0.002 PHE A 133 TRP 0.030 0.002 TRP A 436 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00505 (28291) covalent geometry : angle 0.78800 (38466) SS BOND : bond 0.00456 ( 45) SS BOND : angle 1.76423 ( 90) hydrogen bonds : bond 0.04685 ( 1074) hydrogen bonds : angle 5.94759 ( 2982) link_ALPHA1-4 : bond 0.01638 ( 15) link_ALPHA1-4 : angle 3.07459 ( 45) link_BETA1-4 : bond 0.00341 ( 29) link_BETA1-4 : angle 1.85153 ( 87) link_BETA1-6 : bond 0.01683 ( 3) link_BETA1-6 : angle 2.39623 ( 9) link_NAG-ASN : bond 0.00532 ( 54) link_NAG-ASN : angle 4.10765 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 574 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8604 (mmmm) REVERT: A 111 ASP cc_start: 0.8140 (p0) cc_final: 0.7519 (t70) REVERT: A 129 LYS cc_start: 0.9001 (tttt) cc_final: 0.8512 (ttmm) REVERT: A 224 GLU cc_start: 0.8446 (mp0) cc_final: 0.8156 (mp0) REVERT: A 228 ASP cc_start: 0.8143 (p0) cc_final: 0.7884 (p0) REVERT: A 266 TYR cc_start: 0.8192 (m-80) cc_final: 0.7858 (m-80) REVERT: A 287 ASP cc_start: 0.8690 (t0) cc_final: 0.8322 (t0) REVERT: A 306 PHE cc_start: 0.8373 (m-10) cc_final: 0.7745 (m-10) REVERT: A 456 PHE cc_start: 0.8118 (m-80) cc_final: 0.7803 (m-80) REVERT: A 588 THR cc_start: 0.8957 (m) cc_final: 0.8693 (t) REVERT: A 607 GLN cc_start: 0.8382 (mp10) cc_final: 0.7755 (mp10) REVERT: A 663 ASP cc_start: 0.8387 (t0) cc_final: 0.7983 (t0) REVERT: A 740 MET cc_start: 0.9217 (tpt) cc_final: 0.8974 (tpp) REVERT: A 752 LEU cc_start: 0.9445 (mm) cc_final: 0.9215 (mp) REVERT: A 780 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8457 (mm-30) REVERT: A 819 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 848 ASP cc_start: 0.8453 (t0) cc_final: 0.8039 (t0) REVERT: A 854 LYS cc_start: 0.9445 (tttt) cc_final: 0.9213 (tttt) REVERT: A 856 LYS cc_start: 0.9324 (mptt) cc_final: 0.9060 (mptt) REVERT: A 867 ASP cc_start: 0.8638 (m-30) cc_final: 0.8336 (m-30) REVERT: A 935 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: A 936 ASP cc_start: 0.8845 (m-30) cc_final: 0.8542 (m-30) REVERT: A 1045 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8484 (tptt) REVERT: A 1072 GLU cc_start: 0.8918 (pm20) cc_final: 0.8605 (pm20) REVERT: B 41 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8472 (mmmm) REVERT: B 52 GLN cc_start: 0.8741 (tp40) cc_final: 0.8214 (tp40) REVERT: B 92 PHE cc_start: 0.8639 (t80) cc_final: 0.8417 (t80) REVERT: B 105 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8404 (tp) REVERT: B 200 TYR cc_start: 0.8079 (m-80) cc_final: 0.7793 (m-80) REVERT: B 202 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8619 (mmtm) REVERT: B 218 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 237 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8150 (ptt90) REVERT: B 297 SER cc_start: 0.9245 (m) cc_final: 0.8822 (p) REVERT: B 354 ASN cc_start: 0.8184 (t0) cc_final: 0.7789 (p0) REVERT: B 365 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6893 (p90) REVERT: B 388 ASN cc_start: 0.8491 (t0) cc_final: 0.8162 (t0) REVERT: B 518 LEU cc_start: 0.9299 (mm) cc_final: 0.8961 (tp) REVERT: B 571 ASP cc_start: 0.8865 (t0) cc_final: 0.8252 (t0) REVERT: B 646 ARG cc_start: 0.8436 (ttt90) cc_final: 0.8222 (ttt90) REVERT: B 649 CYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7282 (p) REVERT: B 654 GLU cc_start: 0.8790 (tp30) cc_final: 0.8551 (tp30) REVERT: B 661 GLU cc_start: 0.8471 (pm20) cc_final: 0.8141 (pm20) REVERT: B 675 GLN cc_start: 0.7577 (pp30) cc_final: 0.7357 (pp30) REVERT: B 755 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: B 868 GLU cc_start: 0.8643 (mp0) cc_final: 0.8427 (mp0) REVERT: B 1005 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8670 (tp40) REVERT: B 1010 GLN cc_start: 0.8897 (mt0) cc_final: 0.8615 (mm-40) REVERT: B 1107 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8134 (mtt90) REVERT: C 63 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 129 LYS cc_start: 0.8536 (tttt) cc_final: 0.8318 (ttmt) REVERT: C 191 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7995 (mt-10) REVERT: C 218 GLN cc_start: 0.8353 (tt0) cc_final: 0.8085 (tt0) REVERT: C 224 GLU cc_start: 0.8579 (mp0) cc_final: 0.8161 (mp0) REVERT: C 242 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8323 (mm) REVERT: C 360 ASN cc_start: 0.9070 (t0) cc_final: 0.8618 (t0) REVERT: C 365 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 377 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7143 (t80) REVERT: C 386 LYS cc_start: 0.8813 (mttp) cc_final: 0.8400 (mttp) REVERT: C 516 GLU cc_start: 0.8098 (tp30) cc_final: 0.7736 (tp30) REVERT: C 547 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8711 (mtpp) REVERT: C 564 GLN cc_start: 0.8911 (tp40) cc_final: 0.8597 (tp40) REVERT: C 568 ASP cc_start: 0.8108 (t0) cc_final: 0.7859 (t0) REVERT: C 571 ASP cc_start: 0.8324 (t0) cc_final: 0.7996 (t0) REVERT: C 610 VAL cc_start: 0.9248 (t) cc_final: 0.8956 (m) REVERT: C 613 GLN cc_start: 0.7905 (mt0) cc_final: 0.7619 (mt0) REVERT: C 646 ARG cc_start: 0.9209 (tpp80) cc_final: 0.8607 (ttp80) REVERT: C 654 GLU cc_start: 0.8697 (tt0) cc_final: 0.8376 (pt0) REVERT: C 661 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7690 (tm-30) REVERT: C 755 GLN cc_start: 0.8917 (mp10) cc_final: 0.8599 (mp10) REVERT: C 773 GLU cc_start: 0.8733 (tt0) cc_final: 0.7949 (tm-30) REVERT: C 780 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8437 (mm-30) REVERT: C 950 ASP cc_start: 0.8162 (p0) cc_final: 0.7845 (p0) REVERT: C 957 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7949 (tm-30) outliers start: 93 outliers final: 66 residues processed: 624 average time/residue: 0.1918 time to fit residues: 188.1086 Evaluate side-chains 591 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 516 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 115 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 206 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 394 ASN B 439 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075287 restraints weight = 76962.957| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.05 r_work: 0.3045 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 28437 Z= 0.217 Angle : 0.813 17.502 38859 Z= 0.386 Chirality : 0.049 0.593 4635 Planarity : 0.005 0.066 4827 Dihedral : 10.922 110.161 5704 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 3.86 % Allowed : 14.76 % Favored : 81.38 % 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: -0.78 (0.14), residues: 3324 helix: 1.13 (0.19), residues: 773 sheet: -0.12 (0.18), residues: 683 loop : -1.44 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.020 0.002 TYR C 636 PHE 0.027 0.002 PHE C 342 TRP 0.022 0.002 TRP C 436 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00480 (28291) covalent geometry : angle 0.76133 (38466) SS BOND : bond 0.00413 ( 45) SS BOND : angle 1.67987 ( 90) hydrogen bonds : bond 0.04392 ( 1074) hydrogen bonds : angle 5.76802 ( 2982) link_ALPHA1-4 : bond 0.01666 ( 15) link_ALPHA1-4 : angle 3.25513 ( 45) link_BETA1-4 : bond 0.00315 ( 29) link_BETA1-4 : angle 1.76488 ( 87) link_BETA1-6 : bond 0.01886 ( 3) link_BETA1-6 : angle 2.23441 ( 9) link_NAG-ASN : bond 0.00474 ( 54) link_NAG-ASN : angle 3.82730 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 555 time to evaluate : 1.010 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 41 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8621 (mmmm) REVERT: A 120 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8635 (m) REVERT: A 129 LYS cc_start: 0.8985 (tttt) cc_final: 0.8458 (ttmm) REVERT: A 177 MET cc_start: 0.6913 (ppp) cc_final: 0.6705 (ppp) REVERT: A 190 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8301 (mmm-85) REVERT: A 224 GLU cc_start: 0.8400 (mp0) cc_final: 0.8103 (mp0) REVERT: A 228 ASP cc_start: 0.8109 (p0) cc_final: 0.7821 (p0) REVERT: A 266 TYR cc_start: 0.8204 (m-80) cc_final: 0.7763 (m-80) REVERT: A 287 ASP cc_start: 0.8721 (t0) cc_final: 0.8348 (t0) REVERT: A 306 PHE cc_start: 0.8427 (m-10) cc_final: 0.7881 (m-10) REVERT: A 319 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7697 (tpt170) REVERT: A 421 TYR cc_start: 0.6378 (m-10) cc_final: 0.6133 (m-10) REVERT: A 456 PHE cc_start: 0.7937 (m-80) cc_final: 0.7689 (m-80) REVERT: A 588 THR cc_start: 0.8970 (m) cc_final: 0.8703 (t) REVERT: A 607 GLN cc_start: 0.8372 (mp10) cc_final: 0.7761 (mp10) REVERT: A 658 ASN cc_start: 0.8329 (t0) cc_final: 0.7864 (p0) REVERT: A 663 ASP cc_start: 0.8429 (t0) cc_final: 0.8204 (t0) REVERT: A 740 MET cc_start: 0.9215 (tpt) cc_final: 0.8995 (tpp) REVERT: A 773 GLU cc_start: 0.8564 (tt0) cc_final: 0.8267 (tp30) REVERT: A 780 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8450 (mm-30) REVERT: A 819 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 848 ASP cc_start: 0.8447 (t0) cc_final: 0.7710 (p0) REVERT: A 854 LYS cc_start: 0.9451 (tttt) cc_final: 0.9192 (tttt) REVERT: A 867 ASP cc_start: 0.8628 (m-30) cc_final: 0.8360 (m-30) REVERT: A 935 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: A 1072 GLU cc_start: 0.8923 (pm20) cc_final: 0.8591 (pm20) REVERT: A 1086 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8323 (mtmm) REVERT: A 1107 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8398 (mtt-85) REVERT: B 200 TYR cc_start: 0.8023 (m-80) cc_final: 0.7791 (m-80) REVERT: B 202 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8674 (mmtm) REVERT: B 237 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8157 (ptt90) REVERT: B 297 SER cc_start: 0.9274 (m) cc_final: 0.8845 (p) REVERT: B 354 ASN cc_start: 0.8208 (t0) cc_final: 0.7791 (p0) REVERT: B 365 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6825 (p90) REVERT: B 388 ASN cc_start: 0.8529 (t0) cc_final: 0.8214 (t0) REVERT: B 452 LEU cc_start: 0.8333 (mm) cc_final: 0.8092 (mm) REVERT: B 474 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: B 518 LEU cc_start: 0.9290 (mm) cc_final: 0.8937 (tp) REVERT: B 571 ASP cc_start: 0.8868 (t0) cc_final: 0.8254 (t0) REVERT: B 646 ARG cc_start: 0.8426 (ttt90) cc_final: 0.7843 (mtp180) REVERT: B 654 GLU cc_start: 0.8766 (tp30) cc_final: 0.8551 (tp30) REVERT: B 661 GLU cc_start: 0.8527 (pm20) cc_final: 0.8176 (pm20) REVERT: B 675 GLN cc_start: 0.7612 (pp30) cc_final: 0.7332 (pp30) REVERT: B 755 GLN cc_start: 0.8408 (mp10) cc_final: 0.8131 (mp10) REVERT: B 780 GLU cc_start: 0.9005 (tp30) cc_final: 0.8674 (tp30) REVERT: B 848 ASP cc_start: 0.7518 (t0) cc_final: 0.7098 (p0) REVERT: B 983 ARG cc_start: 0.8501 (mpp80) cc_final: 0.8289 (ptp90) REVERT: B 1005 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8628 (tp40) REVERT: B 1010 GLN cc_start: 0.8895 (mt0) cc_final: 0.8628 (mm-40) REVERT: B 1091 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8051 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8139 (mtt90) REVERT: C 129 LYS cc_start: 0.8600 (tttt) cc_final: 0.8357 (ttmt) REVERT: C 191 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7989 (mt-10) REVERT: C 218 GLN cc_start: 0.8332 (tt0) cc_final: 0.8102 (tt0) REVERT: C 224 GLU cc_start: 0.8626 (mp0) cc_final: 0.8230 (mp0) REVERT: C 298 GLU cc_start: 0.9086 (tp30) cc_final: 0.8884 (tp30) REVERT: C 306 PHE cc_start: 0.8702 (m-80) cc_final: 0.8494 (m-80) REVERT: C 316 SER cc_start: 0.8873 (m) cc_final: 0.8528 (p) REVERT: C 360 ASN cc_start: 0.9091 (t0) cc_final: 0.8637 (t0) REVERT: C 365 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7477 (t80) REVERT: C 377 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7178 (t80) REVERT: C 386 LYS cc_start: 0.8810 (mttp) cc_final: 0.8426 (mttm) REVERT: C 428 ASP cc_start: 0.8597 (t0) cc_final: 0.8394 (t0) REVERT: C 516 GLU cc_start: 0.8169 (tp30) cc_final: 0.7772 (tp30) REVERT: C 547 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8738 (mtpp) REVERT: C 564 GLN cc_start: 0.8886 (tp40) cc_final: 0.8586 (tp40) REVERT: C 571 ASP cc_start: 0.8331 (t0) cc_final: 0.7973 (t0) REVERT: C 610 VAL cc_start: 0.9244 (t) cc_final: 0.8959 (m) REVERT: C 613 GLN cc_start: 0.7899 (mt0) cc_final: 0.7652 (mt0) REVERT: C 646 ARG cc_start: 0.9211 (tpp80) cc_final: 0.8606 (ttp80) REVERT: C 661 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 752 LEU cc_start: 0.9149 (mm) cc_final: 0.8909 (mm) REVERT: C 755 GLN cc_start: 0.8930 (mp10) cc_final: 0.8618 (mp10) REVERT: C 773 GLU cc_start: 0.8691 (tt0) cc_final: 0.7849 (tm-30) REVERT: C 855 PHE cc_start: 0.8865 (m-10) cc_final: 0.8659 (m-10) REVERT: C 918 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 950 ASP cc_start: 0.8152 (p0) cc_final: 0.7813 (p0) REVERT: C 979 ASP cc_start: 0.8892 (t0) cc_final: 0.8673 (t0) outliers start: 113 outliers final: 76 residues processed: 619 average time/residue: 0.1902 time to fit residues: 185.0895 Evaluate side-chains 610 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 526 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 203 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 326 optimal weight: 0.0970 chunk 259 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 954 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.097647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075867 restraints weight = 76443.294| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.03 r_work: 0.3059 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28437 Z= 0.174 Angle : 0.791 17.181 38859 Z= 0.374 Chirality : 0.049 0.603 4635 Planarity : 0.005 0.090 4827 Dihedral : 10.333 108.529 5701 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 3.72 % Allowed : 16.30 % Favored : 79.98 % 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: -0.70 (0.14), residues: 3324 helix: 1.27 (0.19), residues: 772 sheet: -0.12 (0.18), residues: 682 loop : -1.39 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 214 TYR 0.030 0.002 TYR C 636 PHE 0.026 0.002 PHE A 140 TRP 0.029 0.001 TRP C 436 HIS 0.009 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00385 (28291) covalent geometry : angle 0.74038 (38466) SS BOND : bond 0.00633 ( 45) SS BOND : angle 1.69674 ( 90) hydrogen bonds : bond 0.04120 ( 1074) hydrogen bonds : angle 5.65143 ( 2982) link_ALPHA1-4 : bond 0.01610 ( 15) link_ALPHA1-4 : angle 3.31840 ( 45) link_BETA1-4 : bond 0.00307 ( 29) link_BETA1-4 : angle 1.66697 ( 87) link_BETA1-6 : bond 0.02115 ( 3) link_BETA1-6 : angle 2.02606 ( 9) link_NAG-ASN : bond 0.00437 ( 54) link_NAG-ASN : angle 3.67775 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 551 time to evaluate : 1.010 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 41 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8663 (mmmm) REVERT: A 129 LYS cc_start: 0.8879 (tttt) cc_final: 0.8414 (ttmm) REVERT: A 190 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8290 (mmm-85) REVERT: A 195 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8559 (mttt) REVERT: A 224 GLU cc_start: 0.8343 (mp0) cc_final: 0.7961 (mp0) REVERT: A 228 ASP cc_start: 0.8079 (p0) cc_final: 0.7812 (p0) REVERT: A 266 TYR cc_start: 0.8232 (m-80) cc_final: 0.7731 (m-80) REVERT: A 287 ASP cc_start: 0.8713 (t0) cc_final: 0.7759 (t0) REVERT: A 306 PHE cc_start: 0.8442 (m-10) cc_final: 0.7674 (m-10) REVERT: A 319 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7694 (tpt170) REVERT: A 421 TYR cc_start: 0.6478 (m-10) cc_final: 0.6256 (m-10) REVERT: A 456 PHE cc_start: 0.7986 (m-80) cc_final: 0.7751 (m-80) REVERT: A 588 THR cc_start: 0.8983 (m) cc_final: 0.8733 (t) REVERT: A 607 GLN cc_start: 0.8403 (mp10) cc_final: 0.7771 (mp10) REVERT: A 658 ASN cc_start: 0.8331 (t0) cc_final: 0.8058 (p0) REVERT: A 663 ASP cc_start: 0.8463 (t0) cc_final: 0.8217 (t0) REVERT: A 740 MET cc_start: 0.9199 (tpt) cc_final: 0.8987 (tpp) REVERT: A 763 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 780 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8417 (mm-30) REVERT: A 819 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 848 ASP cc_start: 0.8437 (t0) cc_final: 0.7682 (p0) REVERT: A 854 LYS cc_start: 0.9455 (tttt) cc_final: 0.9214 (tttt) REVERT: A 867 ASP cc_start: 0.8621 (m-30) cc_final: 0.8340 (m-30) REVERT: A 935 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: A 1045 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8376 (tptt) REVERT: A 1072 GLU cc_start: 0.8914 (pm20) cc_final: 0.8588 (pm20) REVERT: A 1086 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8255 (mtmm) REVERT: B 52 GLN cc_start: 0.8761 (tp40) cc_final: 0.8199 (tp40) REVERT: B 156 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5320 (mm-30) REVERT: B 176 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6133 (mt) REVERT: B 200 TYR cc_start: 0.8005 (m-80) cc_final: 0.7803 (m-80) REVERT: B 202 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8649 (mmtm) REVERT: B 237 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8167 (ptt90) REVERT: B 297 SER cc_start: 0.9277 (m) cc_final: 0.8866 (p) REVERT: B 354 ASN cc_start: 0.8239 (t0) cc_final: 0.7777 (p0) REVERT: B 365 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6837 (p90) REVERT: B 452 LEU cc_start: 0.8389 (mm) cc_final: 0.8187 (mm) REVERT: B 474 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: B 518 LEU cc_start: 0.9252 (mm) cc_final: 0.9039 (tp) REVERT: B 571 ASP cc_start: 0.8887 (t0) cc_final: 0.8265 (t0) REVERT: B 646 ARG cc_start: 0.8408 (ttt90) cc_final: 0.7808 (mtp180) REVERT: B 654 GLU cc_start: 0.8759 (tp30) cc_final: 0.8536 (tp30) REVERT: B 661 GLU cc_start: 0.8508 (pm20) cc_final: 0.8138 (pm20) REVERT: B 675 GLN cc_start: 0.7586 (pp30) cc_final: 0.7327 (pp30) REVERT: B 755 GLN cc_start: 0.8388 (mp10) cc_final: 0.8088 (mp10) REVERT: B 780 GLU cc_start: 0.9016 (tp30) cc_final: 0.8676 (tp30) REVERT: B 848 ASP cc_start: 0.7601 (t0) cc_final: 0.7155 (p0) REVERT: B 1002 GLN cc_start: 0.8631 (tp40) cc_final: 0.8382 (tp40) REVERT: B 1005 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8609 (tp40) REVERT: B 1010 GLN cc_start: 0.8886 (mt0) cc_final: 0.8624 (mm-40) REVERT: B 1072 GLU cc_start: 0.8786 (pm20) cc_final: 0.8307 (pm20) REVERT: B 1091 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8072 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8467 (mtt180) cc_final: 0.8174 (mtp85) REVERT: C 63 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8518 (p) REVERT: C 129 LYS cc_start: 0.8640 (tttt) cc_final: 0.8258 (ttmt) REVERT: C 191 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8008 (mt-10) REVERT: C 223 LEU cc_start: 0.9123 (mt) cc_final: 0.8895 (mm) REVERT: C 224 GLU cc_start: 0.8618 (mp0) cc_final: 0.8225 (mp0) REVERT: C 242 LEU cc_start: 0.8701 (mm) cc_final: 0.8457 (mm) REVERT: C 298 GLU cc_start: 0.9101 (tp30) cc_final: 0.8893 (tp30) REVERT: C 306 PHE cc_start: 0.8708 (m-80) cc_final: 0.8477 (m-80) REVERT: C 316 SER cc_start: 0.8850 (m) cc_final: 0.8505 (p) REVERT: C 360 ASN cc_start: 0.9076 (t0) cc_final: 0.8585 (t0) REVERT: C 365 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7363 (t80) REVERT: C 377 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6957 (t80) REVERT: C 386 LYS cc_start: 0.8780 (mttp) cc_final: 0.8476 (mttm) REVERT: C 428 ASP cc_start: 0.8588 (t0) cc_final: 0.8317 (t0) REVERT: C 516 GLU cc_start: 0.8130 (tp30) cc_final: 0.7686 (tp30) REVERT: C 547 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8710 (mtpp) REVERT: C 564 GLN cc_start: 0.8866 (tp40) cc_final: 0.8560 (tp40) REVERT: C 571 ASP cc_start: 0.8336 (t0) cc_final: 0.8000 (t0) REVERT: C 610 VAL cc_start: 0.9225 (t) cc_final: 0.8941 (m) REVERT: C 613 GLN cc_start: 0.7886 (mt0) cc_final: 0.7659 (mt0) REVERT: C 646 ARG cc_start: 0.9238 (tpp80) cc_final: 0.8617 (ttp80) REVERT: C 661 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 663 ASP cc_start: 0.8567 (t0) cc_final: 0.8345 (t0) REVERT: C 773 GLU cc_start: 0.8670 (tt0) cc_final: 0.7738 (tm-30) REVERT: C 918 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8631 (mt-10) REVERT: C 950 ASP cc_start: 0.8104 (p0) cc_final: 0.7783 (p0) REVERT: C 979 ASP cc_start: 0.8890 (t0) cc_final: 0.8639 (t0) REVERT: C 1019 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8210 (ttm-80) outliers start: 109 outliers final: 74 residues processed: 612 average time/residue: 0.1771 time to fit residues: 170.7398 Evaluate side-chains 607 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 522 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 255 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 272 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.096840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075181 restraints weight = 76643.226| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.03 r_work: 0.3045 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 28437 Z= 0.203 Angle : 0.793 17.424 38859 Z= 0.374 Chirality : 0.049 0.590 4635 Planarity : 0.005 0.089 4827 Dihedral : 9.969 107.807 5699 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 3.89 % Allowed : 17.15 % Favored : 78.95 % 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: -0.67 (0.14), residues: 3324 helix: 1.28 (0.19), residues: 774 sheet: -0.11 (0.18), residues: 689 loop : -1.38 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 102 TYR 0.024 0.002 TYR C 636 PHE 0.032 0.002 PHE B 338 TRP 0.034 0.001 TRP C 436 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00456 (28291) covalent geometry : angle 0.74393 (38466) SS BOND : bond 0.00540 ( 45) SS BOND : angle 1.78448 ( 90) hydrogen bonds : bond 0.04163 ( 1074) hydrogen bonds : angle 5.60128 ( 2982) link_ALPHA1-4 : bond 0.01638 ( 15) link_ALPHA1-4 : angle 3.26660 ( 45) link_BETA1-4 : bond 0.00300 ( 29) link_BETA1-4 : angle 1.68658 ( 87) link_BETA1-6 : bond 0.02023 ( 3) link_BETA1-6 : angle 1.82692 ( 9) link_NAG-ASN : bond 0.00480 ( 54) link_NAG-ASN : angle 3.62771 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 548 time to evaluate : 0.922 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: A 41 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8686 (mmmm) REVERT: A 115 GLN cc_start: 0.8935 (tp40) cc_final: 0.8684 (tp-100) REVERT: A 129 LYS cc_start: 0.8904 (tttt) cc_final: 0.8424 (ttmm) REVERT: A 190 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8245 (mmm-85) REVERT: A 204 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: A 228 ASP cc_start: 0.8089 (p0) cc_final: 0.7810 (p0) REVERT: A 266 TYR cc_start: 0.8259 (m-80) cc_final: 0.7689 (m-80) REVERT: A 287 ASP cc_start: 0.8723 (t0) cc_final: 0.8360 (t0) REVERT: A 306 PHE cc_start: 0.8459 (m-10) cc_final: 0.7876 (m-10) REVERT: A 319 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7683 (tpt170) REVERT: A 421 TYR cc_start: 0.6546 (m-10) cc_final: 0.6328 (m-10) REVERT: A 588 THR cc_start: 0.8974 (m) cc_final: 0.8727 (t) REVERT: A 607 GLN cc_start: 0.8430 (mp10) cc_final: 0.7821 (mp10) REVERT: A 740 MET cc_start: 0.9213 (tpt) cc_final: 0.9012 (tpp) REVERT: A 763 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 773 GLU cc_start: 0.8525 (tt0) cc_final: 0.8279 (tp30) REVERT: A 780 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8421 (mm-30) REVERT: A 819 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8068 (mt-10) REVERT: A 820 ASP cc_start: 0.8749 (m-30) cc_final: 0.8507 (m-30) REVERT: A 848 ASP cc_start: 0.8411 (t0) cc_final: 0.7627 (p0) REVERT: A 854 LYS cc_start: 0.9456 (tttt) cc_final: 0.9219 (tttt) REVERT: A 867 ASP cc_start: 0.8667 (m-30) cc_final: 0.8356 (m-30) REVERT: A 935 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: A 1041 ASP cc_start: 0.8716 (m-30) cc_final: 0.8274 (m-30) REVERT: A 1045 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8443 (tptt) REVERT: A 1072 GLU cc_start: 0.8921 (pm20) cc_final: 0.8607 (pm20) REVERT: B 52 GLN cc_start: 0.8743 (tp40) cc_final: 0.8173 (tp40) REVERT: B 156 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5617 (mm-30) REVERT: B 202 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8623 (mmtm) REVERT: B 297 SER cc_start: 0.9296 (m) cc_final: 0.8867 (p) REVERT: B 354 ASN cc_start: 0.8173 (t0) cc_final: 0.7751 (p0) REVERT: B 365 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6770 (p90) REVERT: B 474 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: B 571 ASP cc_start: 0.8917 (t0) cc_final: 0.8323 (t0) REVERT: B 654 GLU cc_start: 0.8779 (tp30) cc_final: 0.8576 (tp30) REVERT: B 661 GLU cc_start: 0.8520 (pm20) cc_final: 0.8155 (pm20) REVERT: B 755 GLN cc_start: 0.8445 (mp10) cc_final: 0.8137 (mp10) REVERT: B 773 GLU cc_start: 0.8775 (tp30) cc_final: 0.8570 (tp30) REVERT: B 780 GLU cc_start: 0.9007 (tp30) cc_final: 0.8680 (tp30) REVERT: B 848 ASP cc_start: 0.7644 (t0) cc_final: 0.7226 (p0) REVERT: B 1002 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8345 (tp40) REVERT: B 1005 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8599 (tp40) REVERT: B 1010 GLN cc_start: 0.8889 (mt0) cc_final: 0.8646 (mm-40) REVERT: B 1072 GLU cc_start: 0.8817 (pm20) cc_final: 0.8394 (pm20) REVERT: B 1091 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8119 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8473 (mtt180) cc_final: 0.8211 (mtt90) REVERT: C 63 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8532 (p) REVERT: C 81 ASN cc_start: 0.8906 (m-40) cc_final: 0.8589 (m-40) REVERT: C 129 LYS cc_start: 0.8748 (tttt) cc_final: 0.8356 (ttmt) REVERT: C 224 GLU cc_start: 0.8621 (mp0) cc_final: 0.8233 (mp0) REVERT: C 242 LEU cc_start: 0.8690 (mm) cc_final: 0.8340 (mm) REVERT: C 298 GLU cc_start: 0.9093 (tp30) cc_final: 0.8873 (tp30) REVERT: C 306 PHE cc_start: 0.8755 (m-80) cc_final: 0.8540 (m-80) REVERT: C 316 SER cc_start: 0.8860 (m) cc_final: 0.8509 (p) REVERT: C 360 ASN cc_start: 0.9091 (t0) cc_final: 0.8587 (t0) REVERT: C 365 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7324 (t80) REVERT: C 377 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.7048 (t80) REVERT: C 386 LYS cc_start: 0.8785 (mttp) cc_final: 0.8418 (mttm) REVERT: C 428 ASP cc_start: 0.8540 (t0) cc_final: 0.8282 (t0) REVERT: C 516 GLU cc_start: 0.8126 (tp30) cc_final: 0.7672 (tp30) REVERT: C 547 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8715 (mtpp) REVERT: C 564 GLN cc_start: 0.8851 (tp40) cc_final: 0.8585 (tp40) REVERT: C 571 ASP cc_start: 0.8380 (t0) cc_final: 0.8050 (t0) REVERT: C 610 VAL cc_start: 0.9253 (t) cc_final: 0.8961 (m) REVERT: C 613 GLN cc_start: 0.7860 (mt0) cc_final: 0.7630 (mt0) REVERT: C 646 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8600 (ttp80) REVERT: C 661 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7325 (tm-30) REVERT: C 773 GLU cc_start: 0.8671 (tt0) cc_final: 0.7815 (tm-30) REVERT: C 804 GLN cc_start: 0.9026 (tt0) cc_final: 0.8769 (tp40) REVERT: C 811 LYS cc_start: 0.8513 (tppt) cc_final: 0.8137 (ttmm) REVERT: C 918 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8491 (mt-10) REVERT: C 950 ASP cc_start: 0.8082 (p0) cc_final: 0.7757 (p0) REVERT: C 979 ASP cc_start: 0.8919 (t0) cc_final: 0.8619 (t0) outliers start: 114 outliers final: 88 residues processed: 612 average time/residue: 0.1875 time to fit residues: 179.8862 Evaluate side-chains 618 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 519 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 274 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 204 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076434 restraints weight = 76175.352| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.02 r_work: 0.3076 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 28437 Z= 0.146 Angle : 0.768 16.719 38859 Z= 0.361 Chirality : 0.048 0.607 4635 Planarity : 0.005 0.138 4827 Dihedral : 9.457 107.800 5695 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 3.72 % Allowed : 17.59 % Favored : 78.68 % 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: -0.55 (0.14), residues: 3324 helix: 1.39 (0.19), residues: 776 sheet: -0.12 (0.18), residues: 699 loop : -1.27 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 646 TYR 0.025 0.001 TYR A 351 PHE 0.032 0.002 PHE C 342 TRP 0.026 0.001 TRP C 436 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (28291) covalent geometry : angle 0.72098 (38466) SS BOND : bond 0.00471 ( 45) SS BOND : angle 1.52921 ( 90) hydrogen bonds : bond 0.03899 ( 1074) hydrogen bonds : angle 5.47319 ( 2982) link_ALPHA1-4 : bond 0.01671 ( 15) link_ALPHA1-4 : angle 3.21506 ( 45) link_BETA1-4 : bond 0.00329 ( 29) link_BETA1-4 : angle 1.61120 ( 87) link_BETA1-6 : bond 0.02006 ( 3) link_BETA1-6 : angle 1.86615 ( 9) link_NAG-ASN : bond 0.00445 ( 54) link_NAG-ASN : angle 3.48568 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 544 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8713 (mmmm) REVERT: A 115 GLN cc_start: 0.8858 (tp40) cc_final: 0.8624 (tp-100) REVERT: A 129 LYS cc_start: 0.8865 (tttt) cc_final: 0.8396 (ttmm) REVERT: A 177 MET cc_start: 0.6867 (ppp) cc_final: 0.6403 (tmm) REVERT: A 190 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: A 204 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: A 228 ASP cc_start: 0.8073 (p0) cc_final: 0.7804 (p0) REVERT: A 266 TYR cc_start: 0.8257 (m-80) cc_final: 0.7708 (m-80) REVERT: A 287 ASP cc_start: 0.8685 (t0) cc_final: 0.7811 (t0) REVERT: A 306 PHE cc_start: 0.8448 (m-10) cc_final: 0.7671 (m-10) REVERT: A 319 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7714 (tpt170) REVERT: A 532 ASN cc_start: 0.7405 (p0) cc_final: 0.6908 (p0) REVERT: A 558 LYS cc_start: 0.8275 (pttt) cc_final: 0.7960 (pttt) REVERT: A 588 THR cc_start: 0.8964 (m) cc_final: 0.8706 (t) REVERT: A 607 GLN cc_start: 0.8412 (mp10) cc_final: 0.7798 (mp10) REVERT: A 643 PHE cc_start: 0.8002 (t80) cc_final: 0.7754 (t80) REVERT: A 646 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8006 (mmm-85) REVERT: A 663 ASP cc_start: 0.8353 (t0) cc_final: 0.8041 (t0) REVERT: A 763 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 773 GLU cc_start: 0.8515 (tt0) cc_final: 0.8114 (tp30) REVERT: A 780 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8472 (mm-30) REVERT: A 819 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8023 (mt-10) REVERT: A 848 ASP cc_start: 0.8359 (t0) cc_final: 0.7939 (m-30) REVERT: A 854 LYS cc_start: 0.9443 (tttt) cc_final: 0.9212 (tttt) REVERT: A 867 ASP cc_start: 0.8646 (m-30) cc_final: 0.8422 (m-30) REVERT: A 935 GLN cc_start: 0.9050 (tm130) cc_final: 0.8669 (tm-30) REVERT: A 957 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 1041 ASP cc_start: 0.8715 (m-30) cc_final: 0.8253 (m-30) REVERT: A 1045 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8420 (tptt) REVERT: A 1072 GLU cc_start: 0.8905 (pm20) cc_final: 0.8592 (pm20) REVERT: B 52 GLN cc_start: 0.8709 (tp40) cc_final: 0.8126 (tp40) REVERT: B 156 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.4962 (tp30) REVERT: B 202 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8610 (mmtm) REVERT: B 237 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8053 (ptt-90) REVERT: B 297 SER cc_start: 0.9275 (m) cc_final: 0.8855 (p) REVERT: B 354 ASN cc_start: 0.8156 (t0) cc_final: 0.7721 (p0) REVERT: B 365 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6814 (p90) REVERT: B 474 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: B 571 ASP cc_start: 0.8921 (t0) cc_final: 0.8328 (t0) REVERT: B 654 GLU cc_start: 0.8758 (tp30) cc_final: 0.8549 (tp30) REVERT: B 661 GLU cc_start: 0.8436 (pm20) cc_final: 0.8059 (pm20) REVERT: B 765 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8416 (mtm110) REVERT: B 773 GLU cc_start: 0.8792 (tp30) cc_final: 0.8394 (tp30) REVERT: B 780 GLU cc_start: 0.8993 (tp30) cc_final: 0.8661 (tp30) REVERT: B 848 ASP cc_start: 0.7623 (t0) cc_final: 0.7217 (p0) REVERT: B 1002 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: B 1005 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8571 (tp40) REVERT: B 1019 ARG cc_start: 0.8329 (ttt90) cc_final: 0.7946 (ttt90) REVERT: B 1091 ARG cc_start: 0.8448 (ttm110) cc_final: 0.8114 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8160 (mtt90) REVERT: C 63 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8500 (p) REVERT: C 81 ASN cc_start: 0.8960 (m-40) cc_final: 0.8588 (m-40) REVERT: C 129 LYS cc_start: 0.8715 (tttt) cc_final: 0.8253 (ttmt) REVERT: C 223 LEU cc_start: 0.9104 (mp) cc_final: 0.8852 (mm) REVERT: C 224 GLU cc_start: 0.8623 (mp0) cc_final: 0.8236 (mp0) REVERT: C 242 LEU cc_start: 0.8682 (mm) cc_final: 0.8335 (mm) REVERT: C 298 GLU cc_start: 0.9102 (tp30) cc_final: 0.8886 (tp30) REVERT: C 306 PHE cc_start: 0.8741 (m-80) cc_final: 0.8412 (m-80) REVERT: C 316 SER cc_start: 0.8863 (m) cc_final: 0.8495 (p) REVERT: C 360 ASN cc_start: 0.9068 (t0) cc_final: 0.8566 (t0) REVERT: C 365 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7202 (t80) REVERT: C 377 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7026 (t80) REVERT: C 386 LYS cc_start: 0.8766 (mttp) cc_final: 0.8389 (mttm) REVERT: C 428 ASP cc_start: 0.8485 (t0) cc_final: 0.8232 (t0) REVERT: C 516 GLU cc_start: 0.8048 (tp30) cc_final: 0.7615 (tp30) REVERT: C 547 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8689 (mtpp) REVERT: C 564 GLN cc_start: 0.8837 (tp40) cc_final: 0.8570 (tp40) REVERT: C 571 ASP cc_start: 0.8351 (t0) cc_final: 0.8024 (t0) REVERT: C 610 VAL cc_start: 0.9236 (t) cc_final: 0.8950 (m) REVERT: C 613 GLN cc_start: 0.7843 (mt0) cc_final: 0.7620 (mt0) REVERT: C 646 ARG cc_start: 0.9226 (tpp80) cc_final: 0.8594 (ttp80) REVERT: C 661 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 773 GLU cc_start: 0.8623 (tt0) cc_final: 0.7517 (tm-30) REVERT: C 777 ASN cc_start: 0.8660 (m-40) cc_final: 0.7472 (m110) REVERT: C 804 GLN cc_start: 0.9001 (tt0) cc_final: 0.8790 (tp40) REVERT: C 811 LYS cc_start: 0.8473 (tppt) cc_final: 0.8125 (ttmm) REVERT: C 918 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8606 (mt-10) REVERT: C 950 ASP cc_start: 0.8068 (p0) cc_final: 0.7733 (p0) REVERT: C 979 ASP cc_start: 0.8915 (t0) cc_final: 0.8597 (t0) REVERT: C 1019 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8262 (ttm-80) REVERT: C 1091 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8328 (mtp85) outliers start: 109 outliers final: 77 residues processed: 610 average time/residue: 0.1867 time to fit residues: 179.8477 Evaluate side-chains 602 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 514 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 2 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 293 optimal weight: 0.0770 chunk 320 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 115 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.098162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076458 restraints weight = 76633.854| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.04 r_work: 0.3075 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 28437 Z= 0.153 Angle : 0.778 16.678 38859 Z= 0.366 Chirality : 0.048 0.596 4635 Planarity : 0.004 0.072 4827 Dihedral : 8.916 107.682 5692 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 3.66 % Allowed : 18.38 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3324 helix: 1.44 (0.19), residues: 771 sheet: -0.14 (0.18), residues: 692 loop : -1.20 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.025 0.001 TYR A 351 PHE 0.036 0.002 PHE B 338 TRP 0.029 0.001 TRP B 436 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00341 (28291) covalent geometry : angle 0.73289 (38466) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.54938 ( 90) hydrogen bonds : bond 0.03858 ( 1074) hydrogen bonds : angle 5.43920 ( 2982) link_ALPHA1-4 : bond 0.01700 ( 15) link_ALPHA1-4 : angle 3.29175 ( 45) link_BETA1-4 : bond 0.00309 ( 29) link_BETA1-4 : angle 1.59434 ( 87) link_BETA1-6 : bond 0.01867 ( 3) link_BETA1-6 : angle 1.83120 ( 9) link_NAG-ASN : bond 0.00430 ( 54) link_NAG-ASN : angle 3.44282 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 531 time to evaluate : 1.057 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: A 41 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8718 (mmmm) REVERT: A 102 ARG cc_start: 0.7321 (mmm-85) cc_final: 0.7086 (mmm-85) REVERT: A 129 LYS cc_start: 0.8869 (tttt) cc_final: 0.8346 (ttmm) REVERT: A 190 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8150 (mmm-85) REVERT: A 204 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: A 228 ASP cc_start: 0.8079 (p0) cc_final: 0.7818 (p0) REVERT: A 287 ASP cc_start: 0.8691 (t0) cc_final: 0.8313 (t0) REVERT: A 319 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7686 (tpt170) REVERT: A 532 ASN cc_start: 0.7372 (p0) cc_final: 0.6875 (p0) REVERT: A 558 LYS cc_start: 0.8284 (pttt) cc_final: 0.7922 (pttt) REVERT: A 588 THR cc_start: 0.8980 (m) cc_final: 0.8765 (t) REVERT: A 607 GLN cc_start: 0.8442 (mp10) cc_final: 0.7831 (mp10) REVERT: A 643 PHE cc_start: 0.8020 (t80) cc_final: 0.7810 (t80) REVERT: A 646 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8134 (mmm-85) REVERT: A 780 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8486 (mm-30) REVERT: A 819 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 848 ASP cc_start: 0.8341 (t0) cc_final: 0.7931 (m-30) REVERT: A 854 LYS cc_start: 0.9440 (tttt) cc_final: 0.9189 (tttt) REVERT: A 867 ASP cc_start: 0.8643 (m-30) cc_final: 0.8387 (m-30) REVERT: A 935 GLN cc_start: 0.9071 (tm130) cc_final: 0.8695 (tm-30) REVERT: A 957 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 1041 ASP cc_start: 0.8731 (m-30) cc_final: 0.8221 (m-30) REVERT: A 1045 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8459 (tptt) REVERT: A 1072 GLU cc_start: 0.8924 (pm20) cc_final: 0.8629 (pm20) REVERT: B 52 GLN cc_start: 0.8693 (tp40) cc_final: 0.8114 (tp40) REVERT: B 156 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5361 (tp30) REVERT: B 202 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8625 (mmtm) REVERT: B 237 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7795 (ptp90) REVERT: B 297 SER cc_start: 0.9266 (m) cc_final: 0.8852 (p) REVERT: B 354 ASN cc_start: 0.8171 (t0) cc_final: 0.7711 (p0) REVERT: B 365 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6811 (p90) REVERT: B 474 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: B 571 ASP cc_start: 0.8917 (t0) cc_final: 0.8325 (t0) REVERT: B 633 TRP cc_start: 0.8812 (p-90) cc_final: 0.8476 (p-90) REVERT: B 654 GLU cc_start: 0.8769 (tp30) cc_final: 0.8553 (tp30) REVERT: B 661 GLU cc_start: 0.8402 (pm20) cc_final: 0.8027 (pm20) REVERT: B 773 GLU cc_start: 0.8795 (tp30) cc_final: 0.8510 (tp30) REVERT: B 780 GLU cc_start: 0.9011 (tp30) cc_final: 0.8709 (tp30) REVERT: B 820 ASP cc_start: 0.8908 (t0) cc_final: 0.8628 (m-30) REVERT: B 848 ASP cc_start: 0.7662 (t0) cc_final: 0.7200 (p0) REVERT: B 1005 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8576 (tp40) REVERT: B 1091 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8153 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8158 (mtt90) REVERT: C 129 LYS cc_start: 0.8703 (tttt) cc_final: 0.8376 (ttmt) REVERT: C 223 LEU cc_start: 0.9101 (mp) cc_final: 0.8854 (mm) REVERT: C 224 GLU cc_start: 0.8619 (mp0) cc_final: 0.8237 (mp0) REVERT: C 242 LEU cc_start: 0.8670 (mm) cc_final: 0.8319 (mm) REVERT: C 298 GLU cc_start: 0.9103 (tp30) cc_final: 0.8874 (tp30) REVERT: C 316 SER cc_start: 0.8869 (m) cc_final: 0.8499 (p) REVERT: C 360 ASN cc_start: 0.9067 (t0) cc_final: 0.8521 (t0) REVERT: C 365 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7160 (t80) REVERT: C 377 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6950 (t80) REVERT: C 386 LYS cc_start: 0.8828 (mttp) cc_final: 0.8458 (mttm) REVERT: C 428 ASP cc_start: 0.8446 (t0) cc_final: 0.8190 (t0) REVERT: C 516 GLU cc_start: 0.7996 (tp30) cc_final: 0.7547 (tp30) REVERT: C 547 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8684 (mtpp) REVERT: C 564 GLN cc_start: 0.8843 (tp40) cc_final: 0.8578 (tp40) REVERT: C 571 ASP cc_start: 0.8362 (t0) cc_final: 0.8034 (t0) REVERT: C 610 VAL cc_start: 0.9232 (t) cc_final: 0.8941 (m) REVERT: C 613 GLN cc_start: 0.7872 (mt0) cc_final: 0.7653 (mt0) REVERT: C 646 ARG cc_start: 0.9249 (tpp80) cc_final: 0.8615 (ttp80) REVERT: C 661 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7364 (tm-30) REVERT: C 755 GLN cc_start: 0.8808 (mp10) cc_final: 0.8586 (mp10) REVERT: C 773 GLU cc_start: 0.8588 (tt0) cc_final: 0.7464 (tm-30) REVERT: C 777 ASN cc_start: 0.8656 (m-40) cc_final: 0.7428 (m110) REVERT: C 811 LYS cc_start: 0.8468 (tppt) cc_final: 0.8148 (ttmm) REVERT: C 918 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8585 (mt-10) REVERT: C 950 ASP cc_start: 0.8068 (p0) cc_final: 0.7727 (p0) REVERT: C 979 ASP cc_start: 0.8941 (t0) cc_final: 0.8615 (t0) REVERT: C 1019 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8281 (ttm-80) REVERT: C 1072 GLU cc_start: 0.8477 (pp20) cc_final: 0.8050 (pp20) REVERT: C 1091 ARG cc_start: 0.8620 (mtp85) cc_final: 0.8340 (mtp85) outliers start: 107 outliers final: 78 residues processed: 597 average time/residue: 0.1898 time to fit residues: 178.2657 Evaluate side-chains 601 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 515 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 259 optimal weight: 0.8980 chunk 64 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 242 optimal weight: 0.5980 chunk 170 optimal weight: 0.1980 chunk 47 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 125 ASN B 207 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.098562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076914 restraints weight = 76305.927| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.03 r_work: 0.3081 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28437 Z= 0.140 Angle : 0.771 16.445 38859 Z= 0.365 Chirality : 0.048 0.604 4635 Planarity : 0.004 0.065 4827 Dihedral : 8.470 107.279 5691 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 3.25 % Allowed : 19.10 % Favored : 77.66 % 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: -0.43 (0.14), residues: 3324 helix: 1.44 (0.19), residues: 771 sheet: -0.09 (0.18), residues: 697 loop : -1.14 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.026 0.001 TYR A 351 PHE 0.037 0.002 PHE B 338 TRP 0.029 0.001 TRP C 436 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (28291) covalent geometry : angle 0.72588 (38466) SS BOND : bond 0.00437 ( 45) SS BOND : angle 1.42662 ( 90) hydrogen bonds : bond 0.03762 ( 1074) hydrogen bonds : angle 5.37662 ( 2982) link_ALPHA1-4 : bond 0.01703 ( 15) link_ALPHA1-4 : angle 3.50161 ( 45) link_BETA1-4 : bond 0.00339 ( 29) link_BETA1-4 : angle 1.55220 ( 87) link_BETA1-6 : bond 0.01800 ( 3) link_BETA1-6 : angle 1.84197 ( 9) link_NAG-ASN : bond 0.00432 ( 54) link_NAG-ASN : angle 3.40399 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 540 time to evaluate : 0.818 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 41 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8734 (mmmm) REVERT: A 129 LYS cc_start: 0.8761 (tttt) cc_final: 0.8419 (tttt) REVERT: A 190 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8179 (mmm-85) REVERT: A 224 GLU cc_start: 0.8245 (mp0) cc_final: 0.7908 (mp0) REVERT: A 228 ASP cc_start: 0.8137 (p0) cc_final: 0.7844 (p0) REVERT: A 287 ASP cc_start: 0.8690 (t0) cc_final: 0.7980 (m-30) REVERT: A 532 ASN cc_start: 0.7420 (p0) cc_final: 0.6927 (p0) REVERT: A 558 LYS cc_start: 0.8248 (pttt) cc_final: 0.7868 (pttt) REVERT: A 588 THR cc_start: 0.8967 (m) cc_final: 0.8746 (t) REVERT: A 607 GLN cc_start: 0.8418 (mp10) cc_final: 0.7807 (mp10) REVERT: A 646 ARG cc_start: 0.8665 (mtp180) cc_final: 0.7994 (mmm-85) REVERT: A 780 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8478 (mm-30) REVERT: A 819 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 848 ASP cc_start: 0.8334 (t0) cc_final: 0.7708 (m-30) REVERT: A 854 LYS cc_start: 0.9429 (tttt) cc_final: 0.9180 (tttt) REVERT: A 867 ASP cc_start: 0.8674 (m-30) cc_final: 0.8409 (m-30) REVERT: A 935 GLN cc_start: 0.9074 (tm130) cc_final: 0.8692 (tm-30) REVERT: A 1041 ASP cc_start: 0.8750 (m-30) cc_final: 0.8232 (m-30) REVERT: A 1045 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8447 (tptt) REVERT: A 1072 GLU cc_start: 0.8917 (pm20) cc_final: 0.8622 (pm20) REVERT: B 52 GLN cc_start: 0.8677 (tp40) cc_final: 0.8126 (tp40) REVERT: B 156 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5716 (tp30) REVERT: B 202 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8659 (mmtm) REVERT: B 237 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7853 (ptp90) REVERT: B 297 SER cc_start: 0.9247 (m) cc_final: 0.8834 (p) REVERT: B 354 ASN cc_start: 0.8144 (t0) cc_final: 0.7662 (p0) REVERT: B 365 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6762 (p90) REVERT: B 452 LEU cc_start: 0.8626 (mm) cc_final: 0.8355 (mm) REVERT: B 474 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7494 (pp30) REVERT: B 571 ASP cc_start: 0.8949 (t0) cc_final: 0.8362 (t0) REVERT: B 633 TRP cc_start: 0.8818 (p-90) cc_final: 0.8569 (p-90) REVERT: B 646 ARG cc_start: 0.8396 (ttt90) cc_final: 0.7837 (mtp180) REVERT: B 654 GLU cc_start: 0.8703 (tp30) cc_final: 0.8484 (tp30) REVERT: B 661 GLU cc_start: 0.8385 (pm20) cc_final: 0.8008 (pm20) REVERT: B 692 ILE cc_start: 0.9205 (tt) cc_final: 0.8709 (pt) REVERT: B 773 GLU cc_start: 0.8814 (tp30) cc_final: 0.8494 (tp30) REVERT: B 780 GLU cc_start: 0.8985 (tp30) cc_final: 0.8684 (tp30) REVERT: B 820 ASP cc_start: 0.8842 (t0) cc_final: 0.8559 (m-30) REVERT: B 848 ASP cc_start: 0.7591 (t0) cc_final: 0.7226 (p0) REVERT: B 1005 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8575 (tp40) REVERT: B 1091 ARG cc_start: 0.8469 (ttm170) cc_final: 0.8158 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8193 (mtt90) REVERT: C 129 LYS cc_start: 0.8730 (tttt) cc_final: 0.8263 (ttmt) REVERT: C 218 GLN cc_start: 0.8292 (mt0) cc_final: 0.7973 (mt0) REVERT: C 223 LEU cc_start: 0.9109 (mp) cc_final: 0.8848 (mm) REVERT: C 224 GLU cc_start: 0.8611 (mp0) cc_final: 0.8223 (mp0) REVERT: C 242 LEU cc_start: 0.8636 (mm) cc_final: 0.8374 (mm) REVERT: C 298 GLU cc_start: 0.9080 (tp30) cc_final: 0.8850 (tp30) REVERT: C 306 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: C 316 SER cc_start: 0.8850 (m) cc_final: 0.8474 (p) REVERT: C 360 ASN cc_start: 0.9020 (t0) cc_final: 0.8476 (t0) REVERT: C 377 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6865 (t80) REVERT: C 386 LYS cc_start: 0.8817 (mttp) cc_final: 0.8434 (mttm) REVERT: C 428 ASP cc_start: 0.8430 (t0) cc_final: 0.8174 (t0) REVERT: C 486 PHE cc_start: 0.8194 (t80) cc_final: 0.7803 (t80) REVERT: C 516 GLU cc_start: 0.7919 (tp30) cc_final: 0.7482 (tp30) REVERT: C 547 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8633 (mtpp) REVERT: C 564 GLN cc_start: 0.8846 (tp40) cc_final: 0.8474 (tp40) REVERT: C 571 ASP cc_start: 0.8325 (t0) cc_final: 0.7993 (t0) REVERT: C 610 VAL cc_start: 0.9204 (t) cc_final: 0.8912 (m) REVERT: C 613 GLN cc_start: 0.7837 (mt0) cc_final: 0.7613 (mt0) REVERT: C 646 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8601 (ttp80) REVERT: C 661 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 755 GLN cc_start: 0.8786 (mp10) cc_final: 0.8583 (mp10) REVERT: C 773 GLU cc_start: 0.8574 (tt0) cc_final: 0.7392 (tm-30) REVERT: C 777 ASN cc_start: 0.8614 (m-40) cc_final: 0.7235 (m110) REVERT: C 811 LYS cc_start: 0.8472 (tppt) cc_final: 0.8173 (ttmm) REVERT: C 918 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8591 (mt-10) REVERT: C 950 ASP cc_start: 0.8061 (p0) cc_final: 0.7737 (p0) REVERT: C 953 ASN cc_start: 0.8779 (m-40) cc_final: 0.8509 (m-40) REVERT: C 979 ASP cc_start: 0.8961 (t0) cc_final: 0.8634 (t0) REVERT: C 988 GLU cc_start: 0.7928 (tp30) cc_final: 0.7609 (tp30) REVERT: C 1019 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8230 (ttm-80) REVERT: C 1072 GLU cc_start: 0.8457 (pp20) cc_final: 0.8024 (pp20) REVERT: C 1091 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8320 (mtp85) outliers start: 95 outliers final: 79 residues processed: 595 average time/residue: 0.1949 time to fit residues: 184.0995 Evaluate side-chains 612 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 527 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 214 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 296 optimal weight: 0.5980 chunk 239 optimal weight: 0.2980 chunk 187 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 226 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 164 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.098737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.077132 restraints weight = 76389.027| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.02 r_work: 0.3086 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28437 Z= 0.139 Angle : 0.781 17.663 38859 Z= 0.368 Chirality : 0.048 0.602 4635 Planarity : 0.004 0.065 4827 Dihedral : 8.231 106.746 5687 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 3.04 % Allowed : 19.58 % Favored : 77.38 % 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: -0.43 (0.14), residues: 3324 helix: 1.41 (0.19), residues: 776 sheet: -0.13 (0.18), residues: 701 loop : -1.10 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.029 0.001 TYR A 421 PHE 0.035 0.002 PHE B 86 TRP 0.023 0.001 TRP C 436 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (28291) covalent geometry : angle 0.73790 (38466) SS BOND : bond 0.00432 ( 45) SS BOND : angle 1.35486 ( 90) hydrogen bonds : bond 0.03726 ( 1074) hydrogen bonds : angle 5.38492 ( 2982) link_ALPHA1-4 : bond 0.01656 ( 15) link_ALPHA1-4 : angle 3.43450 ( 45) link_BETA1-4 : bond 0.00331 ( 29) link_BETA1-4 : angle 1.53971 ( 87) link_BETA1-6 : bond 0.01757 ( 3) link_BETA1-6 : angle 1.79812 ( 9) link_NAG-ASN : bond 0.00448 ( 54) link_NAG-ASN : angle 3.34857 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 536 time to evaluate : 1.156 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 41 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8757 (mmmm) REVERT: A 129 LYS cc_start: 0.8885 (tttt) cc_final: 0.8327 (ttmm) REVERT: A 190 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8210 (mmm-85) REVERT: A 224 GLU cc_start: 0.8157 (mp0) cc_final: 0.7758 (mp0) REVERT: A 226 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 228 ASP cc_start: 0.8208 (p0) cc_final: 0.7929 (p0) REVERT: A 287 ASP cc_start: 0.8657 (t0) cc_final: 0.8158 (t0) REVERT: A 306 PHE cc_start: 0.8463 (m-10) cc_final: 0.7287 (m-10) REVERT: A 319 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7621 (tpt170) REVERT: A 532 ASN cc_start: 0.7399 (p0) cc_final: 0.6909 (p0) REVERT: A 558 LYS cc_start: 0.8270 (pttt) cc_final: 0.7828 (pttt) REVERT: A 588 THR cc_start: 0.8957 (m) cc_final: 0.8723 (t) REVERT: A 607 GLN cc_start: 0.8431 (mp10) cc_final: 0.7825 (mp10) REVERT: A 780 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 819 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 848 ASP cc_start: 0.8166 (t0) cc_final: 0.7630 (m-30) REVERT: A 854 LYS cc_start: 0.9385 (tttt) cc_final: 0.9145 (tttt) REVERT: A 867 ASP cc_start: 0.8659 (m-30) cc_final: 0.8363 (m-30) REVERT: A 935 GLN cc_start: 0.9030 (tm130) cc_final: 0.8702 (tm-30) REVERT: A 981 PHE cc_start: 0.7996 (m-80) cc_final: 0.7738 (m-10) REVERT: A 984 LEU cc_start: 0.8702 (mt) cc_final: 0.8492 (mp) REVERT: A 1002 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8538 (tp40) REVERT: A 1005 GLN cc_start: 0.8862 (tp40) cc_final: 0.8584 (tp40) REVERT: A 1072 GLU cc_start: 0.8915 (pm20) cc_final: 0.8619 (pm20) REVERT: B 52 GLN cc_start: 0.8665 (tp40) cc_final: 0.8068 (tp-100) REVERT: B 156 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5860 (tp30) REVERT: B 157 PHE cc_start: 0.5562 (t80) cc_final: 0.5356 (t80) REVERT: B 202 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8657 (mmtm) REVERT: B 207 HIS cc_start: 0.8070 (m170) cc_final: 0.7869 (m170) REVERT: B 237 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.7830 (ptp90) REVERT: B 266 TYR cc_start: 0.8596 (m-80) cc_final: 0.8386 (m-80) REVERT: B 297 SER cc_start: 0.9241 (m) cc_final: 0.8837 (p) REVERT: B 354 ASN cc_start: 0.8141 (t0) cc_final: 0.7631 (p0) REVERT: B 365 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6756 (p90) REVERT: B 452 LEU cc_start: 0.8640 (mm) cc_final: 0.8356 (mm) REVERT: B 474 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7486 (pp30) REVERT: B 571 ASP cc_start: 0.8930 (t0) cc_final: 0.8369 (t0) REVERT: B 633 TRP cc_start: 0.8788 (p-90) cc_final: 0.8544 (p-90) REVERT: B 646 ARG cc_start: 0.8388 (ttt90) cc_final: 0.7811 (mtp180) REVERT: B 654 GLU cc_start: 0.8710 (tp30) cc_final: 0.8506 (tp30) REVERT: B 661 GLU cc_start: 0.8340 (pm20) cc_final: 0.7993 (pm20) REVERT: B 692 ILE cc_start: 0.9201 (tt) cc_final: 0.8687 (pt) REVERT: B 773 GLU cc_start: 0.8823 (tp30) cc_final: 0.8473 (tp30) REVERT: B 780 GLU cc_start: 0.8990 (tp30) cc_final: 0.8697 (tp30) REVERT: B 820 ASP cc_start: 0.8818 (t0) cc_final: 0.8541 (m-30) REVERT: B 848 ASP cc_start: 0.7585 (t0) cc_final: 0.7237 (p0) REVERT: B 994 ASP cc_start: 0.8687 (t0) cc_final: 0.8189 (t0) REVERT: B 1005 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8588 (tp40) REVERT: B 1091 ARG cc_start: 0.8453 (ttm170) cc_final: 0.8144 (mtm-85) REVERT: B 1107 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8214 (mtt90) REVERT: C 129 LYS cc_start: 0.8688 (tttt) cc_final: 0.8296 (ttmt) REVERT: C 218 GLN cc_start: 0.8270 (mt0) cc_final: 0.7947 (mt0) REVERT: C 223 LEU cc_start: 0.9111 (mp) cc_final: 0.8851 (mm) REVERT: C 224 GLU cc_start: 0.8619 (mp0) cc_final: 0.8228 (mp0) REVERT: C 242 LEU cc_start: 0.8640 (mm) cc_final: 0.8376 (mm) REVERT: C 298 GLU cc_start: 0.9083 (tp30) cc_final: 0.8857 (tp30) REVERT: C 316 SER cc_start: 0.8856 (m) cc_final: 0.8486 (p) REVERT: C 360 ASN cc_start: 0.8998 (t0) cc_final: 0.8449 (t0) REVERT: C 386 LYS cc_start: 0.8796 (mttp) cc_final: 0.8415 (mttm) REVERT: C 428 ASP cc_start: 0.8399 (t0) cc_final: 0.8150 (t0) REVERT: C 486 PHE cc_start: 0.8191 (t80) cc_final: 0.7808 (t80) REVERT: C 516 GLU cc_start: 0.7884 (tp30) cc_final: 0.7493 (tp30) REVERT: C 547 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8643 (mtpp) REVERT: C 564 GLN cc_start: 0.8819 (tp40) cc_final: 0.8554 (tp40) REVERT: C 571 ASP cc_start: 0.8313 (t0) cc_final: 0.7998 (t0) REVERT: C 610 VAL cc_start: 0.9217 (t) cc_final: 0.8909 (m) REVERT: C 646 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8872 (tpp80) REVERT: C 661 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 755 GLN cc_start: 0.8782 (mp10) cc_final: 0.8580 (mp10) REVERT: C 773 GLU cc_start: 0.8580 (tt0) cc_final: 0.7375 (tm-30) REVERT: C 777 ASN cc_start: 0.8607 (m-40) cc_final: 0.7225 (m110) REVERT: C 780 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8379 (mm-30) REVERT: C 811 LYS cc_start: 0.8477 (tppt) cc_final: 0.8194 (ttmm) REVERT: C 918 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8581 (mt-10) REVERT: C 950 ASP cc_start: 0.8059 (p0) cc_final: 0.7744 (p0) REVERT: C 953 ASN cc_start: 0.8817 (m-40) cc_final: 0.8568 (m-40) REVERT: C 979 ASP cc_start: 0.8963 (t0) cc_final: 0.8631 (t0) REVERT: C 988 GLU cc_start: 0.7949 (tp30) cc_final: 0.7595 (tp30) REVERT: C 1019 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8223 (ttm-80) REVERT: C 1072 GLU cc_start: 0.8444 (pp20) cc_final: 0.7996 (pp20) REVERT: C 1091 ARG cc_start: 0.8544 (mtp85) cc_final: 0.8279 (mtp85) outliers start: 89 outliers final: 74 residues processed: 588 average time/residue: 0.1874 time to fit residues: 174.4663 Evaluate side-chains 604 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 523 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.098132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076467 restraints weight = 76551.123| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.03 r_work: 0.3072 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 28437 Z= 0.166 Angle : 0.792 16.620 38859 Z= 0.374 Chirality : 0.048 0.588 4635 Planarity : 0.004 0.064 4827 Dihedral : 8.162 106.610 5685 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 2.97 % Allowed : 19.82 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3324 helix: 1.36 (0.19), residues: 775 sheet: -0.11 (0.18), residues: 718 loop : -1.13 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.025 0.001 TYR A 351 PHE 0.040 0.002 PHE B 86 TRP 0.030 0.001 TRP C 436 HIS 0.013 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00375 (28291) covalent geometry : angle 0.74828 (38466) SS BOND : bond 0.00644 ( 45) SS BOND : angle 1.55503 ( 90) hydrogen bonds : bond 0.03789 ( 1074) hydrogen bonds : angle 5.40548 ( 2982) link_ALPHA1-4 : bond 0.01634 ( 15) link_ALPHA1-4 : angle 3.48963 ( 45) link_BETA1-4 : bond 0.00314 ( 29) link_BETA1-4 : angle 1.55831 ( 87) link_BETA1-6 : bond 0.01535 ( 3) link_BETA1-6 : angle 1.72576 ( 9) link_NAG-ASN : bond 0.00434 ( 54) link_NAG-ASN : angle 3.37494 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7190.97 seconds wall clock time: 124 minutes 12.14 seconds (7452.14 seconds total)