Starting phenix.real_space_refine on Tue Jun 24 04:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7to4_26029/06_2025/7to4_26029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to4_26029/06_2025/7to4_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_26029/06_2025/7to4_26029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to4_26029/06_2025/7to4_26029.map" model { file = "/net/cci-nas-00/data/ceres_data/7to4_26029/06_2025/7to4_26029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to4_26029/06_2025/7to4_26029.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 2.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.57, per 1000 atoms: 0.71 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: 8.32 Conformation dependent library (CDL) restraints added in 3.5 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: 4.32 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: 15.09 Time building geometry restraints manager: 9.70 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 1162 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1162 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1162 or resid 1301 through 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.550 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: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 73.340 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (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 TRP 0.144 0.026 TRP A 104 HIS 0.022 0.007 HIS A1159 PHE 0.097 0.016 PHE B 898 TYR 0.120 0.021 TYR B 660 ARG 0.019 0.001 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.01661 ( 54) link_NAG-ASN : angle 12.81470 ( 162) 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) hydrogen bonds : bond 0.17076 ( 1074) hydrogen bonds : angle 8.55754 ( 2982) link_BETA1-6 : bond 0.01663 ( 3) link_BETA1-6 : angle 2.43629 ( 9) SS BOND : bond 0.01337 ( 45) SS BOND : angle 2.61879 ( 90) covalent geometry : bond 0.01472 (28291) covalent geometry : angle 1.89904 (38466) *********************** 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 : 3.611 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: 0.7665 (Cg_endo) cc_final: 0.7387 (Cg_exo) REVERT: A 52 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8067 (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: 0.8507 (mm) REVERT: A 224 GLU cc_start: 0.8442 (mp0) cc_final: 0.8187 (mp0) REVERT: A 228 ASP cc_start: 0.7630 (p0) cc_final: 0.7415 (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 380 TYR cc_start: 0.6165 (t80) cc_final: 0.5772 (t80) REVERT: A 424 LYS cc_start: 0.5081 (tptt) cc_final: 0.4573 (tttm) REVERT: A 541 PHE cc_start: 0.6328 (p90) cc_final: 0.5760 (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: 0.8737 (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: 0.9034 (tttt) REVERT: A 856 LYS cc_start: 0.9159 (mptt) cc_final: 0.8887 (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: 0.8111 (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: 0.8506 (p) REVERT: A 1005 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7964 (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: 0.7340 (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: 0.8305 (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: 0.8813 (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 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: 0.8482 (m110) REVERT: B 755 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: B 765 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8014 (ttm-80) REVERT: B 780 GLU cc_start: 0.8653 (tp30) cc_final: 0.8252 (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: 0.8195 (t0) REVERT: B 1005 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8516 (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: 0.5891 (m-80) REVERT: C 102 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6547 (mtp180) REVERT: C 154 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 175 PHE cc_start: 0.6191 (t80) cc_final: 0.5544 (m-80) REVERT: C 207 HIS cc_start: 0.7974 (t-90) cc_final: 0.7683 (t70) 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: 0.8122 (mp0) REVERT: C 320 VAL cc_start: 0.8948 (t) cc_final: 0.8451 (m) REVERT: C 360 ASN cc_start: 0.8931 (t0) cc_final: 0.8662 (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: 0.7192 (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: 0.7983 (m-10) REVERT: C 564 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8336 (tp40) REVERT: C 565 PHE cc_start: 0.8909 (m-80) cc_final: 0.8682 (m-10) REVERT: C 568 ASP cc_start: 0.7860 (t0) cc_final: 0.7525 (t0) REVERT: C 571 ASP cc_start: 0.7858 (t0) cc_final: 0.7431 (t0) REVERT: C 577 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8579 (ttm170) REVERT: C 584 ILE cc_start: 0.8900 (mm) cc_final: 0.8411 (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: 0.7616 (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: 0.8552 (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: 0.8636 (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: 0.8001 (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: 0.9208 (t) REVERT: C 1019 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (ttt-90) outliers start: 76 outliers final: 13 residues processed: 793 average time/residue: 0.4584 time to fit residues: 550.1187 Evaluate side-chains 627 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 599 time to evaluate : 3.074 ------------------------------------------------------------------------------- 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 214 GLU 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 281 optimal weight: 0.0670 chunk 252 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN 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 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077546 restraints weight = 76265.640| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.08 r_work: 0.3096 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28437 Z= 0.170 Angle : 0.883 17.748 38859 Z= 0.426 Chirality : 0.053 0.638 4635 Planarity : 0.005 0.050 4827 Dihedral : 12.731 110.744 5747 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 2.84 % Allowed : 11.24 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3324 helix: 0.51 (0.18), residues: 782 sheet: -0.09 (0.19), residues: 603 loop : -1.43 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.009 0.001 HIS B 207 PHE 0.046 0.002 PHE A 133 TYR 0.034 0.002 TYR C 636 ARG 0.013 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 54) link_NAG-ASN : angle 4.64199 ( 162) link_ALPHA1-4 : bond 0.01380 ( 15) link_ALPHA1-4 : angle 2.96657 ( 45) link_BETA1-4 : bond 0.00385 ( 29) link_BETA1-4 : angle 1.99562 ( 87) hydrogen bonds : bond 0.04828 ( 1074) hydrogen bonds : angle 6.21405 ( 2982) link_BETA1-6 : bond 0.01602 ( 3) link_BETA1-6 : angle 2.08934 ( 9) SS BOND : bond 0.00483 ( 45) SS BOND : angle 1.84562 ( 90) covalent geometry : bond 0.00367 (28291) covalent geometry : angle 0.81744 (38466) *********************** 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 709 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 626 time to evaluate : 3.263 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: 0.7446 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: A 41 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8517 (mmmm) REVERT: A 52 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 62 VAL cc_start: 0.8761 (m) cc_final: 0.8518 (p) REVERT: A 111 ASP cc_start: 0.8220 (p0) cc_final: 0.7468 (t70) REVERT: A 129 LYS cc_start: 0.8848 (tttt) cc_final: 0.8382 (ttmm) REVERT: A 135 PHE cc_start: 0.7222 (m-80) cc_final: 0.7019 (m-80) REVERT: A 190 ARG cc_start: 0.8501 (mmm160) cc_final: 0.7960 (mmm-85) REVERT: A 195 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8239 (ttpt) REVERT: A 224 GLU cc_start: 0.8450 (mp0) cc_final: 0.8194 (mp0) REVERT: A 228 ASP cc_start: 0.8003 (p0) cc_final: 0.7741 (p0) REVERT: A 287 ASP cc_start: 0.8628 (t0) cc_final: 0.8307 (t0) REVERT: A 306 PHE cc_start: 0.8334 (m-10) cc_final: 0.7840 (m-10) REVERT: A 456 PHE cc_start: 0.8256 (m-10) cc_final: 0.8042 (m-10) REVERT: A 565 PHE cc_start: 0.7791 (p90) cc_final: 0.7528 (p90) REVERT: A 588 THR cc_start: 0.8973 (m) cc_final: 0.8718 (t) REVERT: A 607 GLN cc_start: 0.8297 (mp10) cc_final: 0.8088 (mp10) REVERT: A 740 MET cc_start: 0.9164 (tpt) cc_final: 0.8831 (tpp) REVERT: A 752 LEU cc_start: 0.9422 (mm) cc_final: 0.9205 (mp) REVERT: A 773 GLU cc_start: 0.8738 (tt0) cc_final: 0.8353 (tt0) REVERT: A 780 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8487 (mm-30) REVERT: A 819 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 820 ASP cc_start: 0.8625 (t70) cc_final: 0.8411 (m-30) REVERT: A 823 PHE cc_start: 0.8079 (m-80) cc_final: 0.7589 (t80) REVERT: A 848 ASP cc_start: 0.8492 (t0) cc_final: 0.7629 (p0) REVERT: A 849 LEU cc_start: 0.8662 (mt) cc_final: 0.8316 (mm) REVERT: A 851 CYS cc_start: 0.8357 (t) cc_final: 0.8063 (t) REVERT: A 854 LYS cc_start: 0.9452 (tttt) cc_final: 0.9212 (tttt) REVERT: A 856 LYS cc_start: 0.9309 (mptt) cc_final: 0.9018 (mptt) REVERT: A 867 ASP cc_start: 0.8589 (m-30) cc_final: 0.8381 (m-30) REVERT: A 921 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8665 (mtmm) REVERT: A 935 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8645 (tm-30) REVERT: A 950 ASP cc_start: 0.8406 (p0) cc_final: 0.8047 (p0) REVERT: A 969 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8820 (mtpp) REVERT: A 1019 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8242 (ttp-110) REVERT: A 1071 GLN cc_start: 0.8392 (mt0) cc_final: 0.8136 (mt0) REVERT: A 1072 GLU cc_start: 0.8835 (pm20) cc_final: 0.8505 (pm20) REVERT: A 1084 ASP cc_start: 0.8373 (t0) cc_final: 0.8086 (t0) REVERT: A 1148 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6076 (t80) REVERT: B 40 ASP cc_start: 0.8845 (t0) cc_final: 0.8603 (t70) REVERT: B 41 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8421 (mmmm) REVERT: B 52 GLN cc_start: 0.8772 (tp40) cc_final: 0.8294 (tp40) REVERT: B 65 PHE cc_start: 0.8529 (m-10) cc_final: 0.8242 (m-10) REVERT: B 200 TYR cc_start: 0.8150 (m-80) cc_final: 0.7896 (m-80) REVERT: B 202 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8707 (mmtm) REVERT: B 237 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8164 (ptt90) REVERT: B 297 SER cc_start: 0.9262 (m) cc_final: 0.8839 (p) REVERT: B 305 SER cc_start: 0.9155 (t) cc_final: 0.8939 (t) REVERT: B 323 THR cc_start: 0.8870 (t) cc_final: 0.8642 (p) REVERT: B 388 ASN cc_start: 0.8433 (t0) cc_final: 0.8115 (t0) REVERT: B 518 LEU cc_start: 0.9283 (mm) cc_final: 0.8975 (tp) REVERT: B 571 ASP cc_start: 0.8850 (t0) cc_final: 0.8236 (t0) REVERT: B 654 GLU cc_start: 0.8715 (tp30) cc_final: 0.8472 (tp30) REVERT: B 661 GLU cc_start: 0.8470 (pm20) cc_final: 0.8140 (pm20) REVERT: B 675 GLN cc_start: 0.7595 (pp30) cc_final: 0.7383 (pp30) REVERT: B 752 LEU cc_start: 0.9381 (mt) cc_final: 0.8664 (mp) REVERT: B 765 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8436 (mtm110) REVERT: B 868 GLU cc_start: 0.8605 (mp0) cc_final: 0.8328 (mp0) REVERT: B 900 MET cc_start: 0.8852 (tpp) cc_final: 0.8641 (mtp) REVERT: B 912 THR cc_start: 0.9259 (m) cc_final: 0.9057 (p) REVERT: B 936 ASP cc_start: 0.8431 (m-30) cc_final: 0.8226 (m-30) REVERT: B 983 ARG cc_start: 0.8524 (mpp80) cc_final: 0.8266 (ptp90) REVERT: B 1005 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8614 (tp40) REVERT: B 1010 GLN cc_start: 0.8838 (mt0) cc_final: 0.8497 (mm-40) REVERT: C 81 ASN cc_start: 0.8866 (m-40) cc_final: 0.8441 (m-40) REVERT: C 114 THR cc_start: 0.8304 (t) cc_final: 0.8016 (m) REVERT: C 133 PHE cc_start: 0.7730 (m-80) cc_final: 0.7513 (m-80) REVERT: C 154 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: C 175 PHE cc_start: 0.6194 (t80) cc_final: 0.5610 (m-80) REVERT: C 224 GLU cc_start: 0.8548 (mp0) cc_final: 0.8026 (mp0) REVERT: C 242 LEU cc_start: 0.8559 (mm) cc_final: 0.8000 (mm) REVERT: C 360 ASN cc_start: 0.9084 (t0) cc_final: 0.8568 (t0) REVERT: C 377 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7104 (t80) REVERT: C 547 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8701 (mtpp) REVERT: C 564 GLN cc_start: 0.8914 (tp40) cc_final: 0.8628 (tp40) REVERT: C 568 ASP cc_start: 0.7920 (t0) cc_final: 0.7632 (t0) REVERT: C 571 ASP cc_start: 0.8189 (t0) cc_final: 0.7924 (t0) REVERT: C 610 VAL cc_start: 0.9273 (t) cc_final: 0.8999 (m) REVERT: C 613 GLN cc_start: 0.7927 (mt0) cc_final: 0.7669 (mt0) REVERT: C 646 ARG cc_start: 0.9191 (tpp80) cc_final: 0.8980 (tpp80) REVERT: C 661 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7747 (tm-30) REVERT: C 675 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7697 (pp30) REVERT: C 759 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7541 (t80) REVERT: C 773 GLU cc_start: 0.8750 (tt0) cc_final: 0.8059 (tm-30) REVERT: C 855 PHE cc_start: 0.8793 (m-10) cc_final: 0.8528 (m-80) REVERT: C 950 ASP cc_start: 0.8131 (p0) cc_final: 0.7824 (p0) REVERT: C 953 ASN cc_start: 0.8737 (m110) cc_final: 0.8412 (m-40) REVERT: C 957 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 979 ASP cc_start: 0.8869 (t0) cc_final: 0.8603 (t0) REVERT: C 1144 GLU cc_start: 0.8584 (mp0) cc_final: 0.8338 (mp0) outliers start: 83 outliers final: 47 residues processed: 659 average time/residue: 0.4744 time to fit residues: 487.6381 Evaluate side-chains 603 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 550 time to evaluate : 4.802 ------------------------------------------------------------------------------- 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 270 LEU 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 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR 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 827 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 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 382 VAL 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 791 THR Chi-restraints excluded: chain B residue 935 GLN 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 177 MET 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 Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 266 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 281 optimal weight: 0.3980 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 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1002 GLN B 125 ASN B 207 HIS B 751 ASN B 784 GLN B 935 GLN C 183 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.099088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076980 restraints weight = 76371.834| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.09 r_work: 0.3080 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28437 Z= 0.165 Angle : 0.805 16.844 38859 Z= 0.384 Chirality : 0.050 0.595 4635 Planarity : 0.004 0.061 4827 Dihedral : 11.381 109.818 5704 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 2.87 % Allowed : 13.05 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3324 helix: 1.00 (0.19), residues: 785 sheet: -0.06 (0.18), residues: 669 loop : -1.29 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 436 HIS 0.005 0.001 HIS B 519 PHE 0.028 0.002 PHE A 133 TYR 0.033 0.002 TYR C 636 ARG 0.008 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 54) link_NAG-ASN : angle 4.04158 ( 162) link_ALPHA1-4 : bond 0.01627 ( 15) link_ALPHA1-4 : angle 3.00638 ( 45) link_BETA1-4 : bond 0.00306 ( 29) link_BETA1-4 : angle 1.74459 ( 87) hydrogen bonds : bond 0.04365 ( 1074) hydrogen bonds : angle 5.84019 ( 2982) link_BETA1-6 : bond 0.01570 ( 3) link_BETA1-6 : angle 2.31976 ( 9) SS BOND : bond 0.00659 ( 45) SS BOND : angle 1.66350 ( 90) covalent geometry : bond 0.00364 (28291) covalent geometry : angle 0.74895 (38466) *********************** 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 658 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 574 time to evaluate : 6.980 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: 0.9183 (mmmm) cc_final: 0.8644 (mmmm) REVERT: A 99 ASN cc_start: 0.7916 (t0) cc_final: 0.7681 (t0) REVERT: A 111 ASP cc_start: 0.8189 (p0) cc_final: 0.7527 (t70) REVERT: A 129 LYS cc_start: 0.8955 (tttt) cc_final: 0.8498 (ttmm) REVERT: A 190 ARG cc_start: 0.8539 (mmm160) cc_final: 0.7779 (mmm-85) REVERT: A 224 GLU cc_start: 0.8450 (mp0) cc_final: 0.8159 (mp0) REVERT: A 228 ASP cc_start: 0.8129 (p0) cc_final: 0.7872 (p0) REVERT: A 266 TYR cc_start: 0.8192 (m-80) cc_final: 0.7835 (m-80) REVERT: A 287 ASP cc_start: 0.8649 (t0) cc_final: 0.8270 (t0) REVERT: A 319 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7581 (tpt170) REVERT: A 406 GLU cc_start: 0.0813 (OUTLIER) cc_final: 0.0433 (mp0) REVERT: A 456 PHE cc_start: 0.8364 (m-10) cc_final: 0.8160 (m-10) REVERT: A 588 THR cc_start: 0.8963 (m) cc_final: 0.8703 (t) REVERT: A 607 GLN cc_start: 0.8348 (mp10) cc_final: 0.8140 (mp10) REVERT: A 663 ASP cc_start: 0.8303 (t0) cc_final: 0.7919 (t0) REVERT: A 740 MET cc_start: 0.9168 (tpt) cc_final: 0.8947 (tpp) REVERT: A 752 LEU cc_start: 0.9428 (mm) cc_final: 0.9202 (mp) REVERT: A 780 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 819 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 820 ASP cc_start: 0.8601 (t70) cc_final: 0.8363 (m-30) REVERT: A 823 PHE cc_start: 0.8095 (m-80) cc_final: 0.7458 (t80) REVERT: A 848 ASP cc_start: 0.8451 (t0) cc_final: 0.8012 (t0) REVERT: A 854 LYS cc_start: 0.9447 (tttt) cc_final: 0.9213 (tttt) REVERT: A 867 ASP cc_start: 0.8590 (m-30) cc_final: 0.8342 (m-30) REVERT: A 935 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8755 (tm-30) REVERT: A 936 ASP cc_start: 0.8726 (m-30) cc_final: 0.8492 (m-30) REVERT: A 1045 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8471 (tptt) REVERT: A 1072 GLU cc_start: 0.8890 (pm20) cc_final: 0.8582 (pm20) REVERT: B 41 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8463 (mmmm) REVERT: B 52 GLN cc_start: 0.8715 (tp40) cc_final: 0.8209 (tp40) REVERT: B 65 PHE cc_start: 0.8595 (m-10) cc_final: 0.8334 (m-10) REVERT: B 92 PHE cc_start: 0.8641 (t80) cc_final: 0.8417 (t80) REVERT: B 105 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 200 TYR cc_start: 0.8069 (m-80) cc_final: 0.7835 (m-80) REVERT: B 202 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8613 (mmtm) REVERT: B 218 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 237 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8146 (ptt90) REVERT: B 297 SER cc_start: 0.9224 (m) cc_final: 0.8808 (p) REVERT: B 305 SER cc_start: 0.9158 (t) cc_final: 0.8954 (t) REVERT: B 342 PHE cc_start: 0.8201 (m-80) cc_final: 0.7823 (m-80) REVERT: B 354 ASN cc_start: 0.8193 (t0) cc_final: 0.7810 (p0) REVERT: B 388 ASN cc_start: 0.8466 (t0) cc_final: 0.8140 (t0) REVERT: B 452 LEU cc_start: 0.8728 (mp) cc_final: 0.8332 (mt) REVERT: B 518 LEU cc_start: 0.9280 (mm) cc_final: 0.8957 (tp) REVERT: B 533 LEU cc_start: 0.8844 (tt) cc_final: 0.8612 (tt) REVERT: B 571 ASP cc_start: 0.8863 (t0) cc_final: 0.8226 (t0) REVERT: B 646 ARG cc_start: 0.8444 (ttt90) cc_final: 0.8243 (ttt90) REVERT: B 649 CYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7340 (p) REVERT: B 654 GLU cc_start: 0.8752 (tp30) cc_final: 0.8513 (tp30) REVERT: B 661 GLU cc_start: 0.8451 (pm20) cc_final: 0.8130 (pm20) REVERT: B 675 GLN cc_start: 0.7617 (pp30) cc_final: 0.7387 (pp30) REVERT: B 755 GLN cc_start: 0.8545 (pt0) cc_final: 0.8236 (mp10) REVERT: B 765 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.8445 (mtm110) REVERT: B 868 GLU cc_start: 0.8629 (mp0) cc_final: 0.8407 (mp0) REVERT: B 912 THR cc_start: 0.9228 (m) cc_final: 0.9014 (p) REVERT: B 983 ARG cc_start: 0.8467 (mpp80) cc_final: 0.8126 (ptp90) REVERT: B 1005 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8627 (tp40) REVERT: B 1010 GLN cc_start: 0.8876 (mt0) cc_final: 0.8597 (mm-40) REVERT: B 1107 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8166 (mtt90) REVERT: C 63 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 114 THR cc_start: 0.8277 (t) cc_final: 0.8036 (m) REVERT: C 154 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: C 191 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 224 GLU cc_start: 0.8563 (mp0) cc_final: 0.8064 (mp0) REVERT: C 242 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8399 (mm) REVERT: C 360 ASN cc_start: 0.9037 (t0) cc_final: 0.8576 (t0) REVERT: C 377 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7101 (t80) REVERT: C 516 GLU cc_start: 0.8017 (tp30) cc_final: 0.7674 (tp30) REVERT: C 547 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8664 (mtpp) REVERT: C 564 GLN cc_start: 0.8919 (tp40) cc_final: 0.8573 (tp40) REVERT: C 568 ASP cc_start: 0.8085 (t0) cc_final: 0.7872 (t0) REVERT: C 571 ASP cc_start: 0.8304 (t0) cc_final: 0.7948 (t0) REVERT: C 610 VAL cc_start: 0.9238 (t) cc_final: 0.8937 (m) REVERT: C 613 GLN cc_start: 0.7874 (mt0) cc_final: 0.7611 (mt0) REVERT: C 646 ARG cc_start: 0.9218 (tpp80) cc_final: 0.8626 (ttp80) REVERT: C 661 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 752 LEU cc_start: 0.9105 (mm) cc_final: 0.8840 (mm) REVERT: C 755 GLN cc_start: 0.8882 (mp10) cc_final: 0.8562 (mp10) REVERT: C 759 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7520 (t80) REVERT: C 773 GLU cc_start: 0.8670 (tt0) cc_final: 0.7946 (tm-30) REVERT: C 918 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8559 (mt-10) REVERT: C 950 ASP cc_start: 0.8168 (p0) cc_final: 0.7869 (p0) REVERT: C 957 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7933 (tm-30) outliers start: 84 outliers final: 55 residues processed: 622 average time/residue: 0.5841 time to fit residues: 572.1531 Evaluate side-chains 594 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 529 time to evaluate : 4.142 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 406 GLU 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 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 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 208 THR 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 415 THR 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 791 THR Chi-restraints excluded: chain B residue 934 ILE 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 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 324 GLU 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 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 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 178 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 296 optimal weight: 0.2980 chunk 325 optimal weight: 1.9990 chunk 291 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 125 ASN B 207 HIS B 439 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.097228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075454 restraints weight = 76997.933| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.04 r_work: 0.3046 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28437 Z= 0.236 Angle : 0.820 17.646 38859 Z= 0.390 Chirality : 0.050 0.579 4635 Planarity : 0.005 0.070 4827 Dihedral : 10.852 109.959 5702 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 3.96 % Allowed : 14.35 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3324 helix: 1.06 (0.19), residues: 780 sheet: -0.09 (0.18), residues: 678 loop : -1.35 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 436 HIS 0.008 0.001 HIS C 66 PHE 0.032 0.002 PHE C 342 TYR 0.020 0.002 TYR C 636 ARG 0.005 0.001 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 54) link_NAG-ASN : angle 3.86092 ( 162) link_ALPHA1-4 : bond 0.01676 ( 15) link_ALPHA1-4 : angle 3.28814 ( 45) link_BETA1-4 : bond 0.00316 ( 29) link_BETA1-4 : angle 1.79369 ( 87) hydrogen bonds : bond 0.04437 ( 1074) hydrogen bonds : angle 5.78354 ( 2982) link_BETA1-6 : bond 0.01803 ( 3) link_BETA1-6 : angle 2.31944 ( 9) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.77797 ( 90) covalent geometry : bond 0.00523 (28291) covalent geometry : angle 0.76645 (38466) *********************** 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 674 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 558 time to evaluate : 3.215 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: 0.9199 (mmmm) cc_final: 0.8623 (mmmm) REVERT: A 53 ASP cc_start: 0.7806 (t70) cc_final: 0.7412 (t70) REVERT: A 120 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8636 (m) REVERT: A 129 LYS cc_start: 0.8967 (tttt) cc_final: 0.8497 (ttmm) REVERT: A 190 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8020 (mmm-85) REVERT: A 224 GLU cc_start: 0.8413 (mp0) cc_final: 0.8105 (mp0) REVERT: A 228 ASP cc_start: 0.8135 (p0) cc_final: 0.7844 (p0) REVERT: A 266 TYR cc_start: 0.8203 (m-80) cc_final: 0.7788 (m-80) REVERT: A 287 ASP cc_start: 0.8714 (t0) cc_final: 0.8312 (t0) REVERT: A 421 TYR cc_start: 0.6496 (m-10) cc_final: 0.6216 (m-10) REVERT: A 588 THR cc_start: 0.8963 (m) cc_final: 0.8699 (t) REVERT: A 607 GLN cc_start: 0.8356 (mp10) cc_final: 0.7740 (mp10) REVERT: A 658 ASN cc_start: 0.8237 (t0) cc_final: 0.7711 (p0) REVERT: A 663 ASP cc_start: 0.8410 (t0) cc_final: 0.8197 (t0) REVERT: A 740 MET cc_start: 0.9208 (tpt) cc_final: 0.8969 (tpp) REVERT: A 752 LEU cc_start: 0.9440 (mm) cc_final: 0.9201 (mp) REVERT: A 763 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 780 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 819 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 820 ASP cc_start: 0.8607 (t70) cc_final: 0.8399 (t0) REVERT: A 823 PHE cc_start: 0.8111 (m-80) cc_final: 0.7479 (t80) REVERT: A 848 ASP cc_start: 0.8428 (t0) cc_final: 0.7680 (p0) REVERT: A 854 LYS cc_start: 0.9459 (tttt) cc_final: 0.9199 (tttt) REVERT: A 935 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8647 (tm-30) REVERT: A 1045 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8540 (tptt) REVERT: A 1072 GLU cc_start: 0.8936 (pm20) cc_final: 0.8619 (pm20) REVERT: B 52 GLN cc_start: 0.8736 (tp40) cc_final: 0.8153 (tp40) REVERT: B 65 PHE cc_start: 0.8570 (m-10) cc_final: 0.8321 (m-10) REVERT: B 191 GLU cc_start: 0.8222 (mp0) cc_final: 0.8015 (mp0) REVERT: B 200 TYR cc_start: 0.7981 (m-80) cc_final: 0.7775 (m-80) REVERT: B 202 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8588 (mmtm) REVERT: B 218 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 237 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8143 (ptt90) REVERT: B 274 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8219 (m) REVERT: B 293 LEU cc_start: 0.8981 (tp) cc_final: 0.8755 (tt) REVERT: B 297 SER cc_start: 0.9258 (m) cc_final: 0.8822 (p) REVERT: B 342 PHE cc_start: 0.8201 (m-80) cc_final: 0.7877 (m-80) REVERT: B 354 ASN cc_start: 0.8190 (t0) cc_final: 0.7777 (p0) REVERT: B 365 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6890 (p90) REVERT: B 388 ASN cc_start: 0.8507 (t0) cc_final: 0.8191 (t0) REVERT: B 474 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: B 518 LEU cc_start: 0.9309 (mm) cc_final: 0.8955 (tp) REVERT: B 571 ASP cc_start: 0.8892 (t0) cc_final: 0.8278 (t0) REVERT: B 646 ARG cc_start: 0.8435 (ttt90) cc_final: 0.8225 (ttt90) REVERT: B 661 GLU cc_start: 0.8487 (pm20) cc_final: 0.8152 (pm20) REVERT: B 675 GLN cc_start: 0.7626 (pp30) cc_final: 0.7349 (pp30) REVERT: B 755 GLN cc_start: 0.8574 (pt0) cc_final: 0.8242 (mp10) REVERT: B 765 ARG cc_start: 0.8731 (ttm-80) cc_final: 0.8457 (mtm110) REVERT: B 780 GLU cc_start: 0.9007 (tp30) cc_final: 0.8675 (tp30) REVERT: B 848 ASP cc_start: 0.7512 (t0) cc_final: 0.7094 (p0) REVERT: B 912 THR cc_start: 0.9209 (m) cc_final: 0.8963 (p) REVERT: B 1005 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8631 (tp40) REVERT: B 1010 GLN cc_start: 0.8904 (mt0) cc_final: 0.8646 (mm-40) REVERT: B 1091 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8053 (mtm-85) REVERT: C 63 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 114 THR cc_start: 0.8266 (t) cc_final: 0.8036 (m) REVERT: C 129 LYS cc_start: 0.8581 (tttt) cc_final: 0.8371 (ttmt) REVERT: C 218 GLN cc_start: 0.8375 (tt0) cc_final: 0.8109 (tt0) REVERT: C 224 GLU cc_start: 0.8611 (mp0) cc_final: 0.8207 (mp0) REVERT: C 360 ASN cc_start: 0.9063 (t0) cc_final: 0.8610 (t0) REVERT: C 365 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7562 (t80) REVERT: C 377 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7144 (t80) REVERT: C 386 LYS cc_start: 0.8798 (mttp) cc_final: 0.8415 (mttm) REVERT: C 428 ASP cc_start: 0.8584 (t0) cc_final: 0.8346 (t0) REVERT: C 516 GLU cc_start: 0.8139 (tp30) cc_final: 0.7752 (tp30) REVERT: C 547 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8711 (mtpp) REVERT: C 564 GLN cc_start: 0.8895 (tp40) cc_final: 0.8570 (tp40) REVERT: C 571 ASP cc_start: 0.8325 (t0) cc_final: 0.7965 (t0) REVERT: C 610 VAL cc_start: 0.9245 (t) cc_final: 0.8956 (m) REVERT: C 613 GLN cc_start: 0.7871 (mt0) cc_final: 0.7621 (mt0) REVERT: C 646 ARG cc_start: 0.9214 (tpp80) cc_final: 0.8600 (ttp80) REVERT: C 661 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 752 LEU cc_start: 0.9150 (mm) cc_final: 0.8920 (mm) REVERT: C 755 GLN cc_start: 0.8935 (mp10) cc_final: 0.8647 (mp10) REVERT: C 773 GLU cc_start: 0.8667 (tt0) cc_final: 0.7834 (tm-30) REVERT: C 950 ASP cc_start: 0.8167 (p0) cc_final: 0.7846 (p0) REVERT: C 979 ASP cc_start: 0.8907 (t0) cc_final: 0.8691 (t0) outliers start: 116 outliers final: 76 residues processed: 627 average time/residue: 0.4383 time to fit residues: 428.6218 Evaluate side-chains 608 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 523 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 114 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 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 391 CYS 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 762 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 772 VAL 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 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 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR 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 365 TYR Chi-restraints excluded: chain B residue 382 VAL 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 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR 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 16 VAL Chi-restraints excluded: chain C residue 42 VAL 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 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 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 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 Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 276 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 chunk 294 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 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 121 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 125 ASN B 207 HIS B 751 ASN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.098645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.076900 restraints weight = 77028.558| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.98 r_work: 0.3087 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28437 Z= 0.152 Angle : 0.762 16.749 38859 Z= 0.360 Chirality : 0.048 0.606 4635 Planarity : 0.005 0.087 4827 Dihedral : 10.181 107.515 5699 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 3.38 % Allowed : 16.33 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3324 helix: 1.19 (0.19), residues: 788 sheet: -0.03 (0.18), residues: 675 loop : -1.28 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 436 HIS 0.009 0.001 HIS C 954 PHE 0.031 0.002 PHE A 981 TYR 0.028 0.001 TYR C 636 ARG 0.010 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 54) link_NAG-ASN : angle 3.61336 ( 162) link_ALPHA1-4 : bond 0.01617 ( 15) link_ALPHA1-4 : angle 3.26606 ( 45) link_BETA1-4 : bond 0.00318 ( 29) link_BETA1-4 : angle 1.62178 ( 87) hydrogen bonds : bond 0.03965 ( 1074) hydrogen bonds : angle 5.55776 ( 2982) link_BETA1-6 : bond 0.02168 ( 3) link_BETA1-6 : angle 2.04629 ( 9) SS BOND : bond 0.00450 ( 45) SS BOND : angle 1.48044 ( 90) covalent geometry : bond 0.00337 (28291) covalent geometry : angle 0.71247 (38466) *********************** 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 657 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 558 time to evaluate : 2.867 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: 0.9175 (mmmm) cc_final: 0.8704 (mmmm) REVERT: A 99 ASN cc_start: 0.8143 (t0) cc_final: 0.7800 (t0) REVERT: A 129 LYS cc_start: 0.8832 (tttt) cc_final: 0.8320 (tttt) REVERT: A 190 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8021 (mmm-85) REVERT: A 195 LYS cc_start: 0.8407 (mttt) cc_final: 0.8207 (mttt) REVERT: A 224 GLU cc_start: 0.8335 (mp0) cc_final: 0.8068 (mp0) REVERT: A 228 ASP cc_start: 0.8003 (p0) cc_final: 0.7719 (p0) REVERT: A 266 TYR cc_start: 0.8216 (m-80) cc_final: 0.7753 (m-80) REVERT: A 287 ASP cc_start: 0.8664 (t0) cc_final: 0.7746 (t0) REVERT: A 306 PHE cc_start: 0.8395 (m-10) cc_final: 0.7627 (m-10) REVERT: A 319 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7667 (tpt170) REVERT: A 588 THR cc_start: 0.9013 (m) cc_final: 0.8782 (t) REVERT: A 607 GLN cc_start: 0.8385 (mp10) cc_final: 0.7769 (mp10) REVERT: A 658 ASN cc_start: 0.8283 (t0) cc_final: 0.7879 (p0) REVERT: A 663 ASP cc_start: 0.8388 (t0) cc_final: 0.8143 (t0) REVERT: A 740 MET cc_start: 0.9150 (tpt) cc_final: 0.8943 (tpp) REVERT: A 752 LEU cc_start: 0.9407 (mm) cc_final: 0.9156 (mp) REVERT: A 763 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 780 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 819 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 820 ASP cc_start: 0.8542 (t70) cc_final: 0.8223 (t0) REVERT: A 823 PHE cc_start: 0.7896 (m-80) cc_final: 0.7435 (m-10) REVERT: A 848 ASP cc_start: 0.8463 (t0) cc_final: 0.7987 (t0) REVERT: A 854 LYS cc_start: 0.9457 (tttt) cc_final: 0.9219 (tttt) REVERT: A 867 ASP cc_start: 0.8627 (m-30) cc_final: 0.8368 (t0) REVERT: A 935 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: A 1005 GLN cc_start: 0.8858 (tp40) cc_final: 0.8454 (tp40) REVERT: A 1045 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8517 (tptt) REVERT: A 1072 GLU cc_start: 0.8826 (pm20) cc_final: 0.8531 (pm20) REVERT: B 52 GLN cc_start: 0.8671 (tp40) cc_final: 0.8157 (tp40) REVERT: B 176 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5879 (mt) REVERT: B 202 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8630 (mmtm) REVERT: B 237 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8088 (ptt90) REVERT: B 297 SER cc_start: 0.9259 (m) cc_final: 0.8844 (p) REVERT: B 342 PHE cc_start: 0.8044 (m-80) cc_final: 0.7743 (m-80) REVERT: B 354 ASN cc_start: 0.8130 (t0) cc_final: 0.7779 (p0) REVERT: B 365 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6900 (p90) REVERT: B 474 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: B 518 LEU cc_start: 0.9179 (mm) cc_final: 0.8963 (tp) REVERT: B 539 VAL cc_start: 0.8858 (m) cc_final: 0.8628 (m) REVERT: B 571 ASP cc_start: 0.8873 (t0) cc_final: 0.8235 (t0) REVERT: B 646 ARG cc_start: 0.8409 (ttt90) cc_final: 0.7872 (mtp180) REVERT: B 661 GLU cc_start: 0.8393 (pm20) cc_final: 0.8075 (pm20) REVERT: B 765 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8376 (mtm110) REVERT: B 780 GLU cc_start: 0.9019 (tp30) cc_final: 0.8700 (tp30) REVERT: B 848 ASP cc_start: 0.7466 (t0) cc_final: 0.7133 (p0) REVERT: B 900 MET cc_start: 0.9048 (mmm) cc_final: 0.8589 (mtp) REVERT: B 912 THR cc_start: 0.9162 (m) cc_final: 0.8951 (p) REVERT: B 1002 GLN cc_start: 0.8601 (tp40) cc_final: 0.8224 (tp40) REVERT: B 1005 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8572 (tp40) REVERT: B 1010 GLN cc_start: 0.8876 (mt0) cc_final: 0.8642 (mm-40) REVERT: B 1091 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8050 (mtm-85) REVERT: C 63 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8543 (p) REVERT: C 129 LYS cc_start: 0.8583 (tttt) cc_final: 0.8348 (ttmt) REVERT: C 218 GLN cc_start: 0.8338 (tt0) cc_final: 0.8111 (tt0) REVERT: C 224 GLU cc_start: 0.8581 (mp0) cc_final: 0.8201 (mp0) REVERT: C 236 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8691 (p) REVERT: C 242 LEU cc_start: 0.8599 (mm) cc_final: 0.8385 (mm) REVERT: C 360 ASN cc_start: 0.8973 (t0) cc_final: 0.8440 (t0) REVERT: C 365 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7365 (t80) REVERT: C 377 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7114 (t80) REVERT: C 386 LYS cc_start: 0.8779 (mttp) cc_final: 0.8513 (mttm) REVERT: C 428 ASP cc_start: 0.8454 (t0) cc_final: 0.8189 (t0) REVERT: C 516 GLU cc_start: 0.7959 (tp30) cc_final: 0.7633 (tp30) REVERT: C 547 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8728 (mtpp) REVERT: C 564 GLN cc_start: 0.8803 (tp40) cc_final: 0.8514 (tp40) REVERT: C 571 ASP cc_start: 0.8253 (t0) cc_final: 0.7908 (t0) REVERT: C 610 VAL cc_start: 0.9238 (t) cc_final: 0.8951 (m) REVERT: C 613 GLN cc_start: 0.7786 (mt0) cc_final: 0.7580 (mt0) REVERT: C 646 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8628 (tpp80) REVERT: C 661 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 663 ASP cc_start: 0.8507 (t0) cc_final: 0.8302 (t0) REVERT: C 752 LEU cc_start: 0.9116 (mm) cc_final: 0.8847 (mm) REVERT: C 755 GLN cc_start: 0.8797 (mp10) cc_final: 0.8561 (mp10) REVERT: C 773 GLU cc_start: 0.8558 (tt0) cc_final: 0.7613 (tm-30) REVERT: C 777 ASN cc_start: 0.8656 (m-40) cc_final: 0.7631 (m110) REVERT: C 811 LYS cc_start: 0.8460 (tppt) cc_final: 0.8053 (ttmm) REVERT: C 950 ASP cc_start: 0.8159 (p0) cc_final: 0.7769 (p0) REVERT: C 979 ASP cc_start: 0.8891 (t0) cc_final: 0.8663 (t0) REVERT: C 1002 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (tp40) outliers start: 99 outliers final: 73 residues processed: 614 average time/residue: 0.3991 time to fit residues: 381.4269 Evaluate side-chains 609 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 525 time to evaluate : 2.877 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 391 CYS 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 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 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 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 102 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP 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 878 LEU 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 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 233 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 LEU 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 401 VAL 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 759 PHE Chi-restraints excluded: chain C residue 763 LEU 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 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 207 optimal weight: 0.1980 chunk 327 optimal weight: 0.9990 chunk 274 optimal weight: 0.6980 chunk 102 optimal weight: 0.0980 chunk 135 optimal weight: 0.0670 chunk 236 optimal weight: 2.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 751 ASN ** 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 935 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.099657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078080 restraints weight = 76583.153| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.97 r_work: 0.3110 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28437 Z= 0.134 Angle : 0.752 16.297 38859 Z= 0.353 Chirality : 0.047 0.606 4635 Planarity : 0.004 0.074 4827 Dihedral : 9.585 105.706 5699 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 3.83 % Allowed : 16.60 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3324 helix: 1.40 (0.19), residues: 773 sheet: -0.03 (0.18), residues: 699 loop : -1.18 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 436 HIS 0.006 0.001 HIS B 519 PHE 0.030 0.001 PHE A 456 TYR 0.025 0.001 TYR C 636 ARG 0.008 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 54) link_NAG-ASN : angle 3.47813 ( 162) link_ALPHA1-4 : bond 0.01621 ( 15) link_ALPHA1-4 : angle 3.16828 ( 45) link_BETA1-4 : bond 0.00365 ( 29) link_BETA1-4 : angle 1.57166 ( 87) hydrogen bonds : bond 0.03715 ( 1074) hydrogen bonds : angle 5.42811 ( 2982) link_BETA1-6 : bond 0.02179 ( 3) link_BETA1-6 : angle 1.99886 ( 9) SS BOND : bond 0.00362 ( 45) SS BOND : angle 1.29502 ( 90) covalent geometry : bond 0.00293 (28291) covalent geometry : angle 0.70576 (38466) *********************** 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 666 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 554 time to evaluate : 3.604 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 99 ASN cc_start: 0.8081 (t0) cc_final: 0.7811 (t0) REVERT: A 102 ARG cc_start: 0.7250 (mmm-85) cc_final: 0.6571 (mmm-85) REVERT: A 111 ASP cc_start: 0.8099 (p0) cc_final: 0.7765 (p0) REVERT: A 129 LYS cc_start: 0.8812 (tttt) cc_final: 0.8299 (tttt) REVERT: A 177 MET cc_start: 0.6829 (ppp) cc_final: 0.6549 (tmm) REVERT: A 190 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8029 (mmm-85) REVERT: A 224 GLU cc_start: 0.8307 (mp0) cc_final: 0.7961 (mp0) REVERT: A 228 ASP cc_start: 0.7989 (p0) cc_final: 0.7672 (p0) REVERT: A 287 ASP cc_start: 0.8653 (t0) cc_final: 0.7939 (t0) REVERT: A 306 PHE cc_start: 0.8387 (m-10) cc_final: 0.7624 (m-10) REVERT: A 319 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7637 (tpt170) REVERT: A 392 PHE cc_start: 0.7247 (m-10) cc_final: 0.6605 (m-80) REVERT: A 588 THR cc_start: 0.9007 (m) cc_final: 0.8767 (t) REVERT: A 607 GLN cc_start: 0.8376 (mp10) cc_final: 0.7748 (mp10) REVERT: A 658 ASN cc_start: 0.8335 (t0) cc_final: 0.7976 (p0) REVERT: A 763 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 773 GLU cc_start: 0.8355 (tp30) cc_final: 0.8083 (tp30) REVERT: A 780 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8390 (mm-30) REVERT: A 819 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 820 ASP cc_start: 0.8473 (t70) cc_final: 0.8164 (t0) REVERT: A 823 PHE cc_start: 0.7862 (m-80) cc_final: 0.7548 (m-10) REVERT: A 848 ASP cc_start: 0.8412 (t0) cc_final: 0.7952 (m-30) REVERT: A 854 LYS cc_start: 0.9460 (tttt) cc_final: 0.9229 (tttt) REVERT: A 935 GLN cc_start: 0.9033 (tm130) cc_final: 0.8667 (tm-30) REVERT: A 1041 ASP cc_start: 0.8628 (m-30) cc_final: 0.8163 (m-30) REVERT: A 1045 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8606 (tptt) REVERT: A 1072 GLU cc_start: 0.8848 (pm20) cc_final: 0.8548 (pm20) REVERT: B 52 GLN cc_start: 0.8689 (tp40) cc_final: 0.8116 (tp40) REVERT: B 156 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5238 (tp30) REVERT: B 157 PHE cc_start: 0.5860 (t80) cc_final: 0.5379 (t80) REVERT: B 176 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5881 (mt) REVERT: B 202 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8639 (mmtm) REVERT: B 237 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.8083 (ptt90) REVERT: B 274 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 297 SER cc_start: 0.9242 (m) cc_final: 0.8834 (p) REVERT: B 354 ASN cc_start: 0.8104 (t0) cc_final: 0.7780 (p0) REVERT: B 365 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6857 (p90) REVERT: B 452 LEU cc_start: 0.8836 (mp) cc_final: 0.8456 (mt) REVERT: B 474 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: B 571 ASP cc_start: 0.8890 (t0) cc_final: 0.8271 (t0) REVERT: B 646 ARG cc_start: 0.8393 (ttt90) cc_final: 0.7872 (mtp180) REVERT: B 661 GLU cc_start: 0.8348 (pm20) cc_final: 0.8044 (pm20) REVERT: B 765 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8412 (mtm110) REVERT: B 780 GLU cc_start: 0.9043 (tp30) cc_final: 0.8731 (tp30) REVERT: B 848 ASP cc_start: 0.7562 (t0) cc_final: 0.7196 (p0) REVERT: B 900 MET cc_start: 0.9061 (mmm) cc_final: 0.8610 (mtp) REVERT: B 912 THR cc_start: 0.9120 (m) cc_final: 0.8916 (p) REVERT: B 1005 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8547 (tp40) REVERT: B 1010 GLN cc_start: 0.8849 (mt0) cc_final: 0.8537 (mm-40) REVERT: B 1091 ARG cc_start: 0.8357 (ttm110) cc_final: 0.8104 (mtm-85) REVERT: C 63 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 129 LYS cc_start: 0.8547 (tttt) cc_final: 0.8125 (ttmt) REVERT: C 224 GLU cc_start: 0.8540 (mp0) cc_final: 0.8163 (mp0) REVERT: C 236 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8667 (p) REVERT: C 242 LEU cc_start: 0.8605 (mm) cc_final: 0.8342 (mm) REVERT: C 298 GLU cc_start: 0.9002 (tp30) cc_final: 0.8791 (tp30) REVERT: C 316 SER cc_start: 0.8801 (m) cc_final: 0.8459 (p) REVERT: C 360 ASN cc_start: 0.8944 (t0) cc_final: 0.8446 (t0) REVERT: C 365 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7424 (t80) REVERT: C 377 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.7015 (t80) REVERT: C 386 LYS cc_start: 0.8662 (mttp) cc_final: 0.8381 (mttm) REVERT: C 428 ASP cc_start: 0.8457 (t0) cc_final: 0.8194 (t0) REVERT: C 516 GLU cc_start: 0.7919 (tp30) cc_final: 0.7560 (tp30) REVERT: C 547 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8712 (mtpp) REVERT: C 564 GLN cc_start: 0.8796 (tp40) cc_final: 0.8510 (tp40) REVERT: C 571 ASP cc_start: 0.8269 (t0) cc_final: 0.7926 (t0) REVERT: C 610 VAL cc_start: 0.9236 (t) cc_final: 0.8932 (m) REVERT: C 646 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8637 (tpp80) REVERT: C 661 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 663 ASP cc_start: 0.8553 (t0) cc_final: 0.8327 (t0) REVERT: C 752 LEU cc_start: 0.9109 (mm) cc_final: 0.8820 (mm) REVERT: C 755 GLN cc_start: 0.8758 (mp10) cc_final: 0.8524 (mp10) REVERT: C 773 GLU cc_start: 0.8549 (tt0) cc_final: 0.7554 (tm-30) REVERT: C 777 ASN cc_start: 0.8597 (m-40) cc_final: 0.7438 (m110) REVERT: C 811 LYS cc_start: 0.8420 (tppt) cc_final: 0.8102 (ttmm) REVERT: C 935 GLN cc_start: 0.8996 (tt0) cc_final: 0.8574 (tt0) REVERT: C 950 ASP cc_start: 0.8070 (p0) cc_final: 0.7752 (p0) REVERT: C 979 ASP cc_start: 0.8876 (t0) cc_final: 0.8613 (t0) REVERT: C 1002 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7970 (mp10) outliers start: 112 outliers final: 72 residues processed: 624 average time/residue: 0.4063 time to fit residues: 398.4472 Evaluate side-chains 600 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 516 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 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 391 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS 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 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 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 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 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 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 474 GLN Chi-restraints excluded: chain B residue 586 ASP 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 878 LEU 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 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 176 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 236 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 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 759 PHE Chi-restraints excluded: chain C residue 850 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 190 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 256 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 308 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1002 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 394 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076771 restraints weight = 76703.331| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.07 r_work: 0.3082 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28437 Z= 0.164 Angle : 0.763 16.617 38859 Z= 0.360 Chirality : 0.048 0.585 4635 Planarity : 0.004 0.087 4827 Dihedral : 9.237 105.484 5693 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 3.66 % Allowed : 17.32 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3324 helix: 1.30 (0.19), residues: 780 sheet: 0.01 (0.18), residues: 700 loop : -1.15 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.008 0.001 HIS B 207 PHE 0.040 0.002 PHE A 456 TYR 0.023 0.001 TYR C 636 ARG 0.011 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 54) link_NAG-ASN : angle 3.52349 ( 162) link_ALPHA1-4 : bond 0.01687 ( 15) link_ALPHA1-4 : angle 3.20813 ( 45) link_BETA1-4 : bond 0.00290 ( 29) link_BETA1-4 : angle 1.56133 ( 87) hydrogen bonds : bond 0.03838 ( 1074) hydrogen bonds : angle 5.43425 ( 2982) link_BETA1-6 : bond 0.01996 ( 3) link_BETA1-6 : angle 1.86168 ( 9) SS BOND : bond 0.00410 ( 45) SS BOND : angle 1.65806 ( 90) covalent geometry : bond 0.00365 (28291) covalent geometry : angle 0.71471 (38466) *********************** 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 643 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 536 time to evaluate : 3.293 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: 0.9195 (mmmm) cc_final: 0.8686 (mmmm) REVERT: A 99 ASN cc_start: 0.8300 (t0) cc_final: 0.8046 (t0) REVERT: A 115 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8507 (tp-100) REVERT: A 129 LYS cc_start: 0.8839 (tttt) cc_final: 0.8260 (tttt) REVERT: A 190 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8100 (mmm-85) REVERT: A 224 GLU cc_start: 0.8315 (mp0) cc_final: 0.7920 (mp0) REVERT: A 228 ASP cc_start: 0.8060 (p0) cc_final: 0.7763 (p0) REVERT: A 287 ASP cc_start: 0.8701 (t0) cc_final: 0.7914 (t0) REVERT: A 306 PHE cc_start: 0.8446 (m-10) cc_final: 0.7692 (m-10) REVERT: A 392 PHE cc_start: 0.7286 (m-10) cc_final: 0.6594 (m-80) REVERT: A 558 LYS cc_start: 0.8268 (pttt) cc_final: 0.8066 (pttt) REVERT: A 588 THR cc_start: 0.8983 (m) cc_final: 0.8779 (t) REVERT: A 607 GLN cc_start: 0.8404 (mp10) cc_final: 0.7776 (mp10) REVERT: A 658 ASN cc_start: 0.8371 (t0) cc_final: 0.7914 (p0) REVERT: A 763 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 773 GLU cc_start: 0.8407 (tp30) cc_final: 0.8137 (tp30) REVERT: A 780 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 819 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8015 (mt-10) REVERT: A 820 ASP cc_start: 0.8545 (t70) cc_final: 0.8294 (t0) REVERT: A 823 PHE cc_start: 0.7731 (m-80) cc_final: 0.7511 (m-10) REVERT: A 848 ASP cc_start: 0.8421 (t0) cc_final: 0.7959 (m-30) REVERT: A 854 LYS cc_start: 0.9458 (tttt) cc_final: 0.9223 (tttt) REVERT: A 867 ASP cc_start: 0.8573 (m-30) cc_final: 0.8143 (t0) REVERT: A 933 LYS cc_start: 0.9105 (mttm) cc_final: 0.8904 (ttmm) REVERT: A 935 GLN cc_start: 0.9062 (tm130) cc_final: 0.8687 (tm-30) REVERT: A 1019 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8366 (ttp80) REVERT: A 1072 GLU cc_start: 0.8895 (pm20) cc_final: 0.8585 (pm20) REVERT: B 52 GLN cc_start: 0.8733 (tp40) cc_final: 0.8113 (tp40) REVERT: B 156 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5606 (tp30) REVERT: B 176 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6031 (mt) REVERT: B 202 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8623 (mmtm) REVERT: B 237 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8117 (ptt90) REVERT: B 266 TYR cc_start: 0.8554 (m-80) cc_final: 0.8136 (m-80) REVERT: B 274 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 297 SER cc_start: 0.9253 (m) cc_final: 0.8850 (p) REVERT: B 342 PHE cc_start: 0.8194 (m-80) cc_final: 0.7943 (m-80) REVERT: B 354 ASN cc_start: 0.8122 (t0) cc_final: 0.7723 (p0) REVERT: B 365 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6867 (p90) REVERT: B 452 LEU cc_start: 0.8895 (mp) cc_final: 0.8509 (mt) REVERT: B 474 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: B 571 ASP cc_start: 0.8918 (t0) cc_final: 0.8319 (t0) REVERT: B 661 GLU cc_start: 0.8355 (pm20) cc_final: 0.8001 (pm20) REVERT: B 765 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8363 (mtm110) REVERT: B 780 GLU cc_start: 0.9022 (tp30) cc_final: 0.8722 (tp30) REVERT: B 848 ASP cc_start: 0.7633 (t0) cc_final: 0.7206 (p0) REVERT: B 900 MET cc_start: 0.9157 (mmm) cc_final: 0.8737 (mtp) REVERT: B 912 THR cc_start: 0.9147 (m) cc_final: 0.8914 (p) REVERT: B 935 GLN cc_start: 0.8809 (pt0) cc_final: 0.8379 (pp30) REVERT: B 1005 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8591 (tp40) REVERT: B 1091 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8136 (mtm-85) REVERT: C 129 LYS cc_start: 0.8686 (tttt) cc_final: 0.8454 (ttmt) REVERT: C 224 GLU cc_start: 0.8599 (mp0) cc_final: 0.8201 (mp0) REVERT: C 236 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8715 (p) REVERT: C 242 LEU cc_start: 0.8692 (mm) cc_final: 0.8410 (mm) REVERT: C 298 GLU cc_start: 0.9043 (tp30) cc_final: 0.8843 (tp30) REVERT: C 316 SER cc_start: 0.8855 (m) cc_final: 0.8512 (p) REVERT: C 360 ASN cc_start: 0.9008 (t0) cc_final: 0.8441 (t0) REVERT: C 365 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7374 (t80) REVERT: C 377 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7097 (t80) REVERT: C 386 LYS cc_start: 0.8726 (mttp) cc_final: 0.8215 (mmmm) REVERT: C 428 ASP cc_start: 0.8523 (t0) cc_final: 0.8272 (t0) REVERT: C 516 GLU cc_start: 0.8008 (tp30) cc_final: 0.7609 (tp30) REVERT: C 547 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8669 (mtpp) REVERT: C 564 GLN cc_start: 0.8863 (tp40) cc_final: 0.8554 (tp40) REVERT: C 571 ASP cc_start: 0.8334 (t0) cc_final: 0.7996 (t0) REVERT: C 610 VAL cc_start: 0.9236 (t) cc_final: 0.8933 (m) REVERT: C 646 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8596 (ttp80) REVERT: C 661 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 663 ASP cc_start: 0.8579 (t0) cc_final: 0.8318 (t0) REVERT: C 773 GLU cc_start: 0.8603 (tt0) cc_final: 0.7524 (tm-30) REVERT: C 777 ASN cc_start: 0.8653 (m-40) cc_final: 0.7470 (m110) REVERT: C 811 LYS cc_start: 0.8446 (tppt) cc_final: 0.8109 (ttmm) REVERT: C 950 ASP cc_start: 0.8082 (p0) cc_final: 0.7761 (p0) REVERT: C 979 ASP cc_start: 0.8927 (t0) cc_final: 0.8619 (t0) REVERT: C 1002 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8150 (mp10) outliers start: 107 outliers final: 80 residues processed: 599 average time/residue: 0.4134 time to fit residues: 388.5973 Evaluate side-chains 612 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 522 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 391 CYS 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 762 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 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 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 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR 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 474 GLN 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 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 986 LYS 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 128 ILE Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 236 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 125 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 914 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.096481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074902 restraints weight = 76759.063| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.00 r_work: 0.3040 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28437 Z= 0.250 Angle : 0.841 17.483 38859 Z= 0.397 Chirality : 0.052 1.076 4635 Planarity : 0.005 0.083 4827 Dihedral : 9.365 106.641 5693 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 3.69 % Allowed : 17.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3324 helix: 1.17 (0.19), residues: 779 sheet: -0.01 (0.18), residues: 681 loop : -1.27 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 436 HIS 0.008 0.001 HIS C 66 PHE 0.055 0.002 PHE A 456 TYR 0.023 0.002 TYR C 636 ARG 0.006 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 54) link_NAG-ASN : angle 4.04796 ( 162) link_ALPHA1-4 : bond 0.01717 ( 15) link_ALPHA1-4 : angle 3.35209 ( 45) link_BETA1-4 : bond 0.00317 ( 29) link_BETA1-4 : angle 1.71264 ( 87) hydrogen bonds : bond 0.04287 ( 1074) hydrogen bonds : angle 5.57692 ( 2982) link_BETA1-6 : bond 0.01826 ( 3) link_BETA1-6 : angle 1.73512 ( 9) SS BOND : bond 0.00462 ( 45) SS BOND : angle 1.65077 ( 90) covalent geometry : bond 0.00552 (28291) covalent geometry : angle 0.78648 (38466) *********************** 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 644 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 536 time to evaluate : 2.913 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: 0.9211 (mmmm) cc_final: 0.8673 (mmmm) REVERT: A 129 LYS cc_start: 0.8974 (tttt) cc_final: 0.8279 (tttt) REVERT: A 177 MET cc_start: 0.6895 (ppp) cc_final: 0.6575 (tmm) REVERT: A 190 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8318 (mmm160) REVERT: A 204 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: A 228 ASP cc_start: 0.8110 (p0) cc_final: 0.7827 (p0) REVERT: A 287 ASP cc_start: 0.8765 (t0) cc_final: 0.8470 (t0) REVERT: A 319 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7704 (tpt170) REVERT: A 558 LYS cc_start: 0.8200 (pttt) cc_final: 0.7837 (pttt) REVERT: A 588 THR cc_start: 0.8988 (m) cc_final: 0.8762 (t) REVERT: A 607 GLN cc_start: 0.8411 (mp10) cc_final: 0.7853 (mp10) REVERT: A 658 ASN cc_start: 0.8343 (t0) cc_final: 0.7866 (p0) REVERT: A 773 GLU cc_start: 0.8489 (tp30) cc_final: 0.8182 (tp30) REVERT: A 780 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8488 (mm-30) REVERT: A 819 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8068 (mt-10) REVERT: A 823 PHE cc_start: 0.7794 (m-80) cc_final: 0.7571 (m-10) REVERT: A 848 ASP cc_start: 0.8378 (t0) cc_final: 0.7980 (m-30) REVERT: A 854 LYS cc_start: 0.9456 (tttt) cc_final: 0.9222 (tttt) REVERT: A 867 ASP cc_start: 0.8592 (m-30) cc_final: 0.8132 (t0) REVERT: A 935 GLN cc_start: 0.9069 (tm130) cc_final: 0.8704 (tm-30) REVERT: A 1041 ASP cc_start: 0.8743 (m-30) cc_final: 0.8295 (m-30) REVERT: A 1045 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8324 (tptt) REVERT: A 1072 GLU cc_start: 0.8915 (pm20) cc_final: 0.8607 (pm20) REVERT: B 32 PHE cc_start: 0.8682 (m-10) cc_final: 0.8384 (m-10) REVERT: B 156 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5376 (mm-30) REVERT: B 202 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8631 (mmtm) REVERT: B 297 SER cc_start: 0.9283 (m) cc_final: 0.8884 (p) REVERT: B 342 PHE cc_start: 0.8218 (m-80) cc_final: 0.7955 (m-80) REVERT: B 354 ASN cc_start: 0.8157 (t0) cc_final: 0.7740 (p0) REVERT: B 365 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6765 (p90) REVERT: B 452 LEU cc_start: 0.8914 (mp) cc_final: 0.8540 (mt) REVERT: B 474 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7526 (pp30) REVERT: B 571 ASP cc_start: 0.8917 (t0) cc_final: 0.8339 (t0) REVERT: B 661 GLU cc_start: 0.8408 (pm20) cc_final: 0.8050 (pm20) REVERT: B 754 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9110 (mt) REVERT: B 765 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8364 (mtp-110) REVERT: B 780 GLU cc_start: 0.9017 (tp30) cc_final: 0.8687 (tp30) REVERT: B 848 ASP cc_start: 0.7685 (t0) cc_final: 0.7225 (p0) REVERT: B 900 MET cc_start: 0.9128 (mmm) cc_final: 0.8841 (mtp) REVERT: B 912 THR cc_start: 0.9171 (m) cc_final: 0.8915 (p) REVERT: B 935 GLN cc_start: 0.8852 (pt0) cc_final: 0.8444 (pp30) REVERT: B 1005 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8615 (tp40) REVERT: B 1010 GLN cc_start: 0.8894 (mt0) cc_final: 0.8569 (mm-40) REVERT: C 129 LYS cc_start: 0.8722 (tttt) cc_final: 0.8410 (tttt) REVERT: C 224 GLU cc_start: 0.8634 (mp0) cc_final: 0.8219 (mp0) REVERT: C 236 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8752 (p) REVERT: C 242 LEU cc_start: 0.8725 (mm) cc_final: 0.8389 (mm) REVERT: C 298 GLU cc_start: 0.9093 (tp30) cc_final: 0.8887 (tp30) REVERT: C 316 SER cc_start: 0.8892 (m) cc_final: 0.8548 (p) REVERT: C 360 ASN cc_start: 0.9088 (t0) cc_final: 0.8520 (t0) REVERT: C 365 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7394 (t80) REVERT: C 377 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7157 (t80) REVERT: C 386 LYS cc_start: 0.8757 (mttp) cc_final: 0.8377 (mttm) REVERT: C 428 ASP cc_start: 0.8559 (t0) cc_final: 0.8330 (t0) REVERT: C 516 GLU cc_start: 0.8131 (tp30) cc_final: 0.7715 (tp30) REVERT: C 547 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8699 (mtpp) REVERT: C 564 GLN cc_start: 0.8845 (tp40) cc_final: 0.8533 (tp40) REVERT: C 571 ASP cc_start: 0.8363 (t0) cc_final: 0.8039 (t0) REVERT: C 610 VAL cc_start: 0.9239 (t) cc_final: 0.8939 (m) REVERT: C 613 GLN cc_start: 0.7851 (mt0) cc_final: 0.7403 (mp10) REVERT: C 646 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8595 (ttp80) REVERT: C 661 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7498 (tm-30) REVERT: C 663 ASP cc_start: 0.8633 (t0) cc_final: 0.8408 (t0) REVERT: C 773 GLU cc_start: 0.8622 (tt0) cc_final: 0.7719 (tm-30) REVERT: C 780 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8471 (mm-30) REVERT: C 811 LYS cc_start: 0.8495 (tppt) cc_final: 0.8143 (ttmm) REVERT: C 918 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8692 (mt-10) REVERT: C 950 ASP cc_start: 0.8100 (p0) cc_final: 0.7782 (p0) REVERT: C 979 ASP cc_start: 0.8931 (t0) cc_final: 0.8598 (t0) REVERT: C 1002 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8321 (mp10) REVERT: C 1072 GLU cc_start: 0.8520 (pp20) cc_final: 0.8107 (pp20) outliers start: 108 outliers final: 82 residues processed: 595 average time/residue: 0.3895 time to fit residues: 360.9325 Evaluate side-chains 610 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 518 time to evaluate : 2.858 ------------------------------------------------------------------------------- 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 204 TYR 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 391 CYS 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 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 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 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 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 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR 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 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN 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 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU 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 128 ILE Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 236 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 434 ILE 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 941 THR 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 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 9 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 144 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.097179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075611 restraints weight = 76579.223| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.01 r_work: 0.3056 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28437 Z= 0.192 Angle : 0.808 17.070 38859 Z= 0.383 Chirality : 0.051 1.131 4635 Planarity : 0.005 0.067 4827 Dihedral : 8.976 107.531 5690 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 3.25 % Allowed : 18.82 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3324 helix: 1.16 (0.19), residues: 782 sheet: -0.07 (0.18), residues: 680 loop : -1.23 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 436 HIS 0.013 0.001 HIS A1083 PHE 0.049 0.002 PHE A 456 TYR 0.030 0.002 TYR B 655 ARG 0.005 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 54) link_NAG-ASN : angle 3.73026 ( 162) link_ALPHA1-4 : bond 0.01703 ( 15) link_ALPHA1-4 : angle 3.50352 ( 45) link_BETA1-4 : bond 0.00327 ( 29) link_BETA1-4 : angle 1.64275 ( 87) hydrogen bonds : bond 0.04074 ( 1074) hydrogen bonds : angle 5.53492 ( 2982) link_BETA1-6 : bond 0.01702 ( 3) link_BETA1-6 : angle 1.75701 ( 9) SS BOND : bond 0.00450 ( 45) SS BOND : angle 1.60572 ( 90) covalent geometry : bond 0.00425 (28291) covalent geometry : angle 0.75740 (38466) *********************** 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 629 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 534 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8697 (mmmm) REVERT: A 129 LYS cc_start: 0.8993 (tttt) cc_final: 0.8304 (tttt) REVERT: A 190 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8101 (mmm-85) REVERT: A 224 GLU cc_start: 0.8271 (mp0) cc_final: 0.7847 (mp0) REVERT: A 228 ASP cc_start: 0.8135 (p0) cc_final: 0.7852 (p0) REVERT: A 287 ASP cc_start: 0.8750 (t0) cc_final: 0.8388 (t0) REVERT: A 558 LYS cc_start: 0.8172 (pttt) cc_final: 0.7781 (pttt) REVERT: A 588 THR cc_start: 0.9013 (m) cc_final: 0.8800 (t) REVERT: A 607 GLN cc_start: 0.8396 (mp10) cc_final: 0.8187 (mp10) REVERT: A 619 GLU cc_start: 0.7828 (mp0) cc_final: 0.7512 (mp0) REVERT: A 658 ASN cc_start: 0.8342 (t0) cc_final: 0.7918 (p0) REVERT: A 773 GLU cc_start: 0.8479 (tp30) cc_final: 0.8220 (tp30) REVERT: A 780 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8474 (mm-30) REVERT: A 819 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 848 ASP cc_start: 0.8347 (t0) cc_final: 0.7977 (m-30) REVERT: A 854 LYS cc_start: 0.9452 (tttt) cc_final: 0.9230 (tttt) REVERT: A 935 GLN cc_start: 0.9070 (tm130) cc_final: 0.8695 (tm-30) REVERT: A 1019 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8322 (ttp80) REVERT: A 1045 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8346 (tptt) REVERT: A 1072 GLU cc_start: 0.8910 (pm20) cc_final: 0.8587 (pm20) REVERT: B 32 PHE cc_start: 0.8700 (m-10) cc_final: 0.8387 (m-10) REVERT: B 52 GLN cc_start: 0.8729 (tp40) cc_final: 0.8110 (tp40) REVERT: B 156 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5496 (mm-30) REVERT: B 202 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8629 (mmtm) REVERT: B 274 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8203 (m) REVERT: B 297 SER cc_start: 0.9263 (m) cc_final: 0.8851 (p) REVERT: B 342 PHE cc_start: 0.8221 (m-80) cc_final: 0.7911 (m-80) REVERT: B 354 ASN cc_start: 0.8158 (t0) cc_final: 0.7716 (p0) REVERT: B 365 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6737 (p90) REVERT: B 452 LEU cc_start: 0.8904 (mp) cc_final: 0.8557 (mt) REVERT: B 474 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: B 571 ASP cc_start: 0.8924 (t0) cc_final: 0.8337 (t0) REVERT: B 646 ARG cc_start: 0.8374 (ttt90) cc_final: 0.7878 (mtp180) REVERT: B 661 GLU cc_start: 0.8405 (pm20) cc_final: 0.8035 (pm20) REVERT: B 754 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9078 (mt) REVERT: B 765 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8340 (mtp-110) REVERT: B 780 GLU cc_start: 0.8993 (tp30) cc_final: 0.8647 (tp30) REVERT: B 786 LYS cc_start: 0.8704 (mttt) cc_final: 0.8439 (mmmt) REVERT: B 848 ASP cc_start: 0.7698 (t0) cc_final: 0.7230 (p0) REVERT: B 900 MET cc_start: 0.9087 (mmm) cc_final: 0.8801 (mtp) REVERT: B 912 THR cc_start: 0.9166 (m) cc_final: 0.8899 (p) REVERT: B 935 GLN cc_start: 0.8831 (pt0) cc_final: 0.8422 (pp30) REVERT: B 1005 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8576 (tp40) REVERT: B 1010 GLN cc_start: 0.8872 (mt0) cc_final: 0.8554 (mm-40) REVERT: B 1072 GLU cc_start: 0.8806 (pm20) cc_final: 0.8349 (pm20) REVERT: B 1091 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8150 (mtm-85) REVERT: C 129 LYS cc_start: 0.8726 (tttt) cc_final: 0.8397 (ttmt) REVERT: C 224 GLU cc_start: 0.8667 (mp0) cc_final: 0.8269 (mp0) REVERT: C 236 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8689 (p) REVERT: C 242 LEU cc_start: 0.8700 (mm) cc_final: 0.8425 (mm) REVERT: C 298 GLU cc_start: 0.9077 (tp30) cc_final: 0.8866 (tp30) REVERT: C 316 SER cc_start: 0.8885 (m) cc_final: 0.8537 (p) REVERT: C 360 ASN cc_start: 0.9075 (t0) cc_final: 0.8508 (t0) REVERT: C 365 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7255 (t80) REVERT: C 377 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7147 (t80) REVERT: C 386 LYS cc_start: 0.8781 (mttp) cc_final: 0.8395 (mttm) REVERT: C 428 ASP cc_start: 0.8537 (t0) cc_final: 0.8333 (t0) REVERT: C 516 GLU cc_start: 0.8071 (tp30) cc_final: 0.7658 (tp30) REVERT: C 547 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8677 (mtpp) REVERT: C 564 GLN cc_start: 0.8835 (tp40) cc_final: 0.8398 (tp40) REVERT: C 571 ASP cc_start: 0.8354 (t0) cc_final: 0.8041 (t0) REVERT: C 610 VAL cc_start: 0.9252 (t) cc_final: 0.8956 (m) REVERT: C 613 GLN cc_start: 0.7879 (mt0) cc_final: 0.7433 (mp10) REVERT: C 646 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8577 (tpp80) REVERT: C 661 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 663 ASP cc_start: 0.8634 (t0) cc_final: 0.8430 (t0) REVERT: C 755 GLN cc_start: 0.8817 (mp10) cc_final: 0.8604 (mp10) REVERT: C 773 GLU cc_start: 0.8622 (tt0) cc_final: 0.7675 (tm-30) REVERT: C 780 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8377 (mm-30) REVERT: C 811 LYS cc_start: 0.8484 (tppt) cc_final: 0.8172 (ttmm) REVERT: C 918 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8666 (mt-10) REVERT: C 950 ASP cc_start: 0.8106 (p0) cc_final: 0.7786 (p0) REVERT: C 979 ASP cc_start: 0.8930 (t0) cc_final: 0.8599 (t0) REVERT: C 988 GLU cc_start: 0.8029 (tp30) cc_final: 0.7701 (tp30) REVERT: C 1072 GLU cc_start: 0.8482 (pp20) cc_final: 0.8055 (pp20) outliers start: 95 outliers final: 80 residues processed: 592 average time/residue: 0.3924 time to fit residues: 363.6682 Evaluate side-chains 609 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 521 time to evaluate : 3.262 ------------------------------------------------------------------------------- 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 365 TYR Chi-restraints excluded: chain A residue 391 CYS 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 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 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 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR 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 340 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR 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 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1152 LEU 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 128 ILE Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 236 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 434 ILE 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 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 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 317 optimal weight: 3.9990 chunk 212 optimal weight: 0.1980 chunk 27 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 262 optimal weight: 0.0270 chunk 162 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.098093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076499 restraints weight = 76157.764| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.02 r_work: 0.3073 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28437 Z= 0.151 Angle : 0.808 16.695 38859 Z= 0.382 Chirality : 0.051 0.908 4635 Planarity : 0.004 0.063 4827 Dihedral : 8.675 107.456 5686 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 3.01 % Allowed : 19.27 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3324 helix: 1.18 (0.19), residues: 790 sheet: -0.04 (0.18), residues: 682 loop : -1.18 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 436 HIS 0.014 0.001 HIS B 207 PHE 0.046 0.002 PHE A 456 TYR 0.030 0.001 TYR B 655 ARG 0.007 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 54) link_NAG-ASN : angle 3.61046 ( 162) link_ALPHA1-4 : bond 0.01646 ( 15) link_ALPHA1-4 : angle 3.46696 ( 45) link_BETA1-4 : bond 0.00352 ( 29) link_BETA1-4 : angle 1.58679 ( 87) hydrogen bonds : bond 0.03872 ( 1074) hydrogen bonds : angle 5.49833 ( 2982) link_BETA1-6 : bond 0.01646 ( 3) link_BETA1-6 : angle 1.80173 ( 9) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.49981 ( 90) covalent geometry : bond 0.00338 (28291) covalent geometry : angle 0.76047 (38466) ********************** 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: 88 poor density : 537 time to evaluate : 3.161 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: A 41 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8690 (mmmm) REVERT: A 102 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: A 129 LYS cc_start: 0.8740 (tttt) cc_final: 0.8362 (tttt) REVERT: A 190 ARG cc_start: 0.8589 (mmm160) cc_final: 0.8128 (mmm-85) REVERT: A 224 GLU cc_start: 0.8297 (mp0) cc_final: 0.7886 (mp0) REVERT: A 228 ASP cc_start: 0.8109 (p0) cc_final: 0.7832 (p0) REVERT: A 287 ASP cc_start: 0.8704 (t0) cc_final: 0.8324 (t0) REVERT: A 558 LYS cc_start: 0.8112 (pttt) cc_final: 0.7683 (pttt) REVERT: A 588 THR cc_start: 0.8998 (m) cc_final: 0.8779 (t) REVERT: A 619 GLU cc_start: 0.7884 (mp0) cc_final: 0.7589 (mp0) REVERT: A 773 GLU cc_start: 0.8451 (tp30) cc_final: 0.8148 (tp30) REVERT: A 780 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 819 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 848 ASP cc_start: 0.8354 (t0) cc_final: 0.7681 (m-30) REVERT: A 854 LYS cc_start: 0.9440 (tttt) cc_final: 0.9194 (tttt) REVERT: A 867 ASP cc_start: 0.8651 (m-30) cc_final: 0.8269 (t0) REVERT: A 935 GLN cc_start: 0.9075 (tm130) cc_final: 0.8682 (tm-30) REVERT: A 1019 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8276 (ttp80) REVERT: A 1045 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8291 (tptt) REVERT: A 1072 GLU cc_start: 0.8893 (pm20) cc_final: 0.8572 (pm20) REVERT: B 32 PHE cc_start: 0.8650 (m-10) cc_final: 0.8420 (m-10) REVERT: B 52 GLN cc_start: 0.8720 (tp40) cc_final: 0.8123 (tp40) REVERT: B 156 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5320 (mm-30) REVERT: B 202 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8666 (mmtm) REVERT: B 274 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8169 (m) REVERT: B 297 SER cc_start: 0.9244 (m) cc_final: 0.8834 (p) REVERT: B 342 PHE cc_start: 0.8216 (m-80) cc_final: 0.7927 (m-80) REVERT: B 354 ASN cc_start: 0.8172 (t0) cc_final: 0.7685 (p0) REVERT: B 365 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6705 (p90) REVERT: B 452 LEU cc_start: 0.8887 (mp) cc_final: 0.8547 (mt) REVERT: B 474 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: B 571 ASP cc_start: 0.8929 (t0) cc_final: 0.8337 (t0) REVERT: B 646 ARG cc_start: 0.8363 (ttt90) cc_final: 0.7833 (mtp180) REVERT: B 661 GLU cc_start: 0.8374 (pm20) cc_final: 0.7996 (pm20) REVERT: B 692 ILE cc_start: 0.9197 (tt) cc_final: 0.8693 (pt) REVERT: B 765 ARG cc_start: 0.8682 (ttm-80) cc_final: 0.8314 (mtp-110) REVERT: B 780 GLU cc_start: 0.8979 (tp30) cc_final: 0.8644 (tp30) REVERT: B 786 LYS cc_start: 0.8677 (mttt) cc_final: 0.8395 (mmmt) REVERT: B 848 ASP cc_start: 0.7619 (t0) cc_final: 0.7224 (p0) REVERT: B 900 MET cc_start: 0.9055 (mmm) cc_final: 0.8778 (mtp) REVERT: B 912 THR cc_start: 0.9141 (m) cc_final: 0.8871 (p) REVERT: B 935 GLN cc_start: 0.8815 (pt0) cc_final: 0.8403 (pp30) REVERT: B 1005 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8546 (tp40) REVERT: B 1072 GLU cc_start: 0.8790 (pm20) cc_final: 0.8324 (pm20) REVERT: B 1091 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8086 (mtm-85) REVERT: C 129 LYS cc_start: 0.8747 (tttt) cc_final: 0.8323 (ttmm) REVERT: C 224 GLU cc_start: 0.8652 (mp0) cc_final: 0.8259 (mp0) REVERT: C 236 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8641 (p) REVERT: C 242 LEU cc_start: 0.8639 (mm) cc_final: 0.8294 (mm) REVERT: C 298 GLU cc_start: 0.9068 (tp30) cc_final: 0.8855 (tp30) REVERT: C 316 SER cc_start: 0.8865 (m) cc_final: 0.8502 (p) REVERT: C 360 ASN cc_start: 0.9047 (t0) cc_final: 0.8472 (t0) REVERT: C 365 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 377 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7142 (t80) REVERT: C 386 LYS cc_start: 0.8759 (mttp) cc_final: 0.8337 (mttm) REVERT: C 428 ASP cc_start: 0.8519 (t0) cc_final: 0.8307 (t0) REVERT: C 486 PHE cc_start: 0.8206 (t80) cc_final: 0.7814 (t80) REVERT: C 516 GLU cc_start: 0.8025 (tp30) cc_final: 0.7593 (tp30) REVERT: C 547 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8667 (mtpp) REVERT: C 564 GLN cc_start: 0.8833 (tp40) cc_final: 0.8441 (tp40) REVERT: C 571 ASP cc_start: 0.8322 (t0) cc_final: 0.8003 (t0) REVERT: C 610 VAL cc_start: 0.9234 (t) cc_final: 0.8949 (m) REVERT: C 613 GLN cc_start: 0.7855 (mt0) cc_final: 0.7483 (mp10) REVERT: C 646 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8547 (tpp80) REVERT: C 661 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 663 ASP cc_start: 0.8626 (t0) cc_final: 0.8407 (t0) REVERT: C 755 GLN cc_start: 0.8808 (mp10) cc_final: 0.8583 (mp10) REVERT: C 773 GLU cc_start: 0.8598 (tt0) cc_final: 0.7439 (tm-30) REVERT: C 777 ASN cc_start: 0.8631 (m-40) cc_final: 0.7382 (m110) REVERT: C 780 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8421 (mm-30) REVERT: C 811 LYS cc_start: 0.8473 (tppt) cc_final: 0.8171 (ttmm) REVERT: C 851 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7641 (p) REVERT: C 918 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8627 (mt-10) REVERT: C 935 GLN cc_start: 0.8847 (tt0) cc_final: 0.8585 (tt0) REVERT: C 950 ASP cc_start: 0.8074 (p0) cc_final: 0.7759 (p0) REVERT: C 979 ASP cc_start: 0.8934 (t0) cc_final: 0.8601 (t0) REVERT: C 988 GLU cc_start: 0.8013 (tp30) cc_final: 0.7670 (tp30) REVERT: C 1072 GLU cc_start: 0.8447 (pp20) cc_final: 0.8010 (pp20) outliers start: 88 outliers final: 72 residues processed: 590 average time/residue: 0.4002 time to fit residues: 370.0218 Evaluate side-chains 604 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 524 time to evaluate : 3.071 ------------------------------------------------------------------------------- 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 365 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS 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 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 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 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 533 LEU 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 957 GLN Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1152 LEU 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 128 ILE Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 236 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 434 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 851 CYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER 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 3 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075191 restraints weight = 76673.560| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.01 r_work: 0.3049 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28437 Z= 0.209 Angle : 0.830 17.348 38859 Z= 0.393 Chirality : 0.051 0.820 4635 Planarity : 0.005 0.068 4827 Dihedral : 8.673 108.040 5685 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 3.21 % Allowed : 19.34 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3324 helix: 1.16 (0.19), residues: 786 sheet: -0.16 (0.18), residues: 705 loop : -1.21 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP C 436 HIS 0.011 0.001 HIS A1083 PHE 0.046 0.002 PHE A 456 TYR 0.029 0.002 TYR B 655 ARG 0.006 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 54) link_NAG-ASN : angle 3.64177 ( 162) link_ALPHA1-4 : bond 0.01659 ( 15) link_ALPHA1-4 : angle 3.61070 ( 45) link_BETA1-4 : bond 0.00304 ( 29) link_BETA1-4 : angle 1.66610 ( 87) hydrogen bonds : bond 0.04101 ( 1074) hydrogen bonds : angle 5.55058 ( 2982) link_BETA1-6 : bond 0.01599 ( 3) link_BETA1-6 : angle 1.69244 ( 9) SS BOND : bond 0.00674 ( 45) SS BOND : angle 1.76420 ( 90) covalent geometry : bond 0.00467 (28291) covalent geometry : angle 0.78116 (38466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15337.80 seconds wall clock time: 268 minutes 21.50 seconds (16101.50 seconds total)