Starting phenix.real_space_refine on Fri Mar 6 03:51:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d56_27206/03_2026/8d56_27206_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d56_27206/03_2026/8d56_27206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d56_27206/03_2026/8d56_27206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d56_27206/03_2026/8d56_27206.map" model { file = "/net/cci-nas-00/data/ceres_data/8d56_27206/03_2026/8d56_27206_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d56_27206/03_2026/8d56_27206_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 119 5.16 5 C 17602 2.51 5 N 4474 2.21 5 O 5479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27674 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8715 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 51, 'TRANS': 1058} Chain breaks: 4 Chain: "B" Number of atoms: 8820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8820 Classifications: {'peptide': 1124} Link IDs: {'PTRANS': 51, 'TRANS': 1072} Chain breaks: 3 Chain: "C" Number of atoms: 8777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8777 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 51, 'TRANS': 1067} Chain breaks: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.21, per 1000 atoms: 0.22 Number of scatterers: 27674 At special positions: 0 Unit cell: (147.74, 143.59, 219.12, 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 119 16.00 O 5479 8.00 N 4474 7.00 C 17602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.98 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=1.99 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG G 2 " - " MAN G 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG Q 2 " - " MAN Q 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 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 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 331 " " NAG C1403 " - " ASN C 343 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 616 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C1074 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6284 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 44 sheets defined 27.0% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 96 through 99 removed outlier: 3.820A pdb=" N ASN A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.797A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.534A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.360A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.081A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.628A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.734A 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 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.767A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.041A 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 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.590A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.212A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.551A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.564A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.051A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.375A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.555A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.695A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.606A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.663A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.341A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.673A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.662A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 4.335A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.736A pdb=" N ASN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.026A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.606A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.912A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.205A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.629A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 removed outlier: 4.086A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.713A 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 912 through 919 removed outlier: 4.114A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.182A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.652A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.004A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.430A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 31 removed outlier: 8.347A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.238A 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: 5.025A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.621A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.902A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 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 311 through 314 removed outlier: 3.764A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.211A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.964A 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: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.689A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.689A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.272A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.339A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.117A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.654A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.076A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.766A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.253A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.158A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 357 removed outlier: 4.015A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.747A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.765A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.585A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.684A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.317A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.151A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 20 through 31 removed outlier: 3.613A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 69 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 261 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.569A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.361A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.434A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.026A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4679 1.31 - 1.44: 7827 1.44 - 1.57: 15637 1.57 - 1.70: 4 1.70 - 1.82: 149 Bond restraints: 28296 Sorted by residual: bond pdb=" N PHE B 133 " pdb=" CA PHE B 133 " ideal model delta sigma weight residual 1.454 1.394 0.061 1.17e-02 7.31e+03 2.67e+01 bond pdb=" CA PHE B 65 " pdb=" C PHE B 65 " ideal model delta sigma weight residual 1.526 1.465 0.061 1.36e-02 5.41e+03 2.00e+01 bond pdb=" CA ARG C 466 " pdb=" C ARG C 466 " ideal model delta sigma weight residual 1.521 1.569 -0.048 1.20e-02 6.94e+03 1.59e+01 bond pdb=" CA HIS B 207 " pdb=" C HIS B 207 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.18e-02 7.18e+03 1.56e+01 bond pdb=" C GLN C 607 " pdb=" O GLN C 607 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.17e-02 7.31e+03 1.40e+01 ... (remaining 28291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 32162 2.38 - 4.76: 5884 4.76 - 7.14: 397 7.14 - 9.52: 32 9.52 - 11.90: 8 Bond angle restraints: 38483 Sorted by residual: angle pdb=" N SER C 172 " pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 108.45 119.22 -10.77 1.26e+00 6.30e-01 7.31e+01 angle pdb=" C LEU B 216 " pdb=" CA LEU B 216 " pdb=" CB LEU B 216 " ideal model delta sigma weight residual 111.20 116.42 -5.22 7.10e-01 1.98e+00 5.41e+01 angle pdb=" N ARG C 246 " pdb=" CA ARG C 246 " pdb=" C ARG C 246 " ideal model delta sigma weight residual 112.25 102.33 9.92 1.36e+00 5.41e-01 5.32e+01 angle pdb=" N ASN A 125 " pdb=" CA ASN A 125 " pdb=" C ASN A 125 " ideal model delta sigma weight residual 108.32 120.22 -11.90 1.64e+00 3.72e-01 5.26e+01 angle pdb=" N ASN C 125 " pdb=" CA ASN C 125 " pdb=" C ASN C 125 " ideal model delta sigma weight residual 108.45 117.51 -9.06 1.26e+00 6.30e-01 5.17e+01 ... (remaining 38478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 17108 24.76 - 49.52: 746 49.52 - 74.29: 181 74.29 - 99.05: 57 99.05 - 123.81: 41 Dihedral angle restraints: 18133 sinusoidal: 8354 harmonic: 9779 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.88 78.88 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 166.32 -73.32 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CA PRO C 491 " pdb=" C PRO C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 18130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 4563 0.257 - 0.514: 65 0.514 - 0.771: 6 0.771 - 1.028: 0 1.028 - 1.284: 3 Chirality restraints: 4637 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.70e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.68e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.44e+01 ... (remaining 4634 not shown) Planarity restraints: 4872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1402 " 0.208 2.00e-02 2.50e+03 1.73e-01 3.74e+02 pdb=" C7 NAG B1402 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1402 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG B1402 " -0.283 2.00e-02 2.50e+03 pdb=" O7 NAG B1402 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " 0.211 2.00e-02 2.50e+03 1.08e-01 2.92e+02 pdb=" CG TRP B 104 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " -0.099 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " -0.144 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " 0.131 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1407 " 0.158 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B1407 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG B1407 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG B1407 " -0.218 2.00e-02 2.50e+03 pdb=" O7 NAG B1407 " -0.014 2.00e-02 2.50e+03 ... (remaining 4869 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.83: 7600 2.83 - 3.52: 37587 3.52 - 4.21: 65331 4.21 - 4.90: 110578 Nonbonded interactions: 221099 Sorted by model distance: nonbonded pdb=" ND2 ASN C 334 " pdb=" O ASN C 360 " model vdw 1.457 3.120 nonbonded pdb=" CD1 LEU B 452 " pdb=" O ARG B 493 " model vdw 1.606 3.460 nonbonded pdb=" O SER B 112 " pdb=" OE2 GLU B 132 " model vdw 2.048 3.040 nonbonded pdb=" O SER C 98 " pdb=" NH2 ARG C 102 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR C 453 " pdb=" NH1 ARG C 493 " model vdw 2.217 3.120 ... (remaining 221094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 624 or resid 629 through 1407)) selection = (chain 'B' and (resid 14 through 71 or resid 80 through 248 or resid 257 through \ 624 or resid 629 through 835 or resid 848 through 1407)) selection = (chain 'C' and (resid 14 through 248 or resid 257 through 835 or resid 848 throu \ gh 1407)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' 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) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.320 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.012 0.061 28442 Z= 0.737 Angle : 1.777 22.906 38877 Z= 1.153 Chirality : 0.105 1.284 4637 Planarity : 0.013 0.173 4821 Dihedral : 16.187 123.809 11717 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer: Outliers : 2.60 % Allowed : 8.32 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3327 helix: -1.36 (0.16), residues: 752 sheet: -0.00 (0.20), residues: 615 loop : -1.86 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 237 TYR 0.119 0.016 TYR A1138 PHE 0.076 0.010 PHE B 718 TRP 0.211 0.026 TRP B 104 HIS 0.017 0.002 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.01205 (28296) covalent geometry : angle 1.73270 (38483) SS BOND : bond 0.01365 ( 44) SS BOND : angle 2.42009 ( 88) hydrogen bonds : bond 0.18469 ( 1086) hydrogen bonds : angle 8.69994 ( 3102) link_ALPHA1-4 : bond 0.00671 ( 18) link_ALPHA1-4 : angle 2.17633 ( 54) link_BETA1-4 : bond 0.00502 ( 30) link_BETA1-4 : angle 1.73867 ( 90) link_BETA1-6 : bond 0.01014 ( 3) link_BETA1-6 : angle 1.96667 ( 9) link_NAG-ASN : bond 0.02349 ( 51) link_NAG-ASN : angle 6.32611 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 238 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7641 (tt) REVERT: A 365 TYR cc_start: 0.7559 (p90) cc_final: 0.6942 (m-80) REVERT: A 468 ILE cc_start: 0.8327 (pt) cc_final: 0.7705 (mm) REVERT: A 739 THR cc_start: 0.8111 (m) cc_final: 0.7846 (p) REVERT: B 54 LEU cc_start: 0.9269 (mt) cc_final: 0.9049 (mt) REVERT: B 489 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 201 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.4572 (t80) REVERT: C 366 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8741 (p) REVERT: C 375 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6528 (p90) outliers start: 76 outliers final: 17 residues processed: 299 average time/residue: 0.6230 time to fit residues: 218.2106 Evaluate side-chains 123 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 491 PRO Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 394 ASN A 409 GLN A 422 ASN A 474 GLN A 487 ASN A 913 GLN A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 188 ASN B 245 HIS B 317 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 450 ASN B 506 GLN B 613 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 774 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B 957 GLN B1010 GLN B1071 GLN B1159 HIS C 14 GLN C 69 HIS C 196 ASN C 245 HIS C 607 GLN C1002 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.098209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059823 restraints weight = 73714.191| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.67 r_work: 0.2874 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28442 Z= 0.165 Angle : 0.783 12.580 38877 Z= 0.384 Chirality : 0.048 0.317 4637 Planarity : 0.004 0.061 4821 Dihedral : 12.896 112.222 5745 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.74 % Allowed : 11.75 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3327 helix: 0.87 (0.19), residues: 753 sheet: 0.11 (0.18), residues: 718 loop : -1.45 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 454 TYR 0.023 0.002 TYR C1067 PHE 0.019 0.002 PHE A 106 TRP 0.024 0.002 TRP C 152 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00357 (28296) covalent geometry : angle 0.74882 (38483) SS BOND : bond 0.00694 ( 44) SS BOND : angle 1.38718 ( 88) hydrogen bonds : bond 0.05069 ( 1086) hydrogen bonds : angle 6.39787 ( 3102) link_ALPHA1-4 : bond 0.01324 ( 18) link_ALPHA1-4 : angle 2.57665 ( 54) link_BETA1-4 : bond 0.00508 ( 30) link_BETA1-4 : angle 1.45882 ( 90) link_BETA1-6 : bond 0.01524 ( 3) link_BETA1-6 : angle 1.65642 ( 9) link_NAG-ASN : bond 0.00514 ( 51) link_NAG-ASN : angle 3.16154 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 121 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8433 (m-80) cc_final: 0.7917 (m-80) REVERT: A 365 TYR cc_start: 0.7560 (p90) cc_final: 0.6495 (m-80) REVERT: A 452 LEU cc_start: 0.9058 (tp) cc_final: 0.8778 (tm) REVERT: A 468 ILE cc_start: 0.8096 (pt) cc_final: 0.7829 (mt) REVERT: B 245 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6606 (p90) REVERT: B 364 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8183 (t0) REVERT: B 429 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6750 (p90) REVERT: B 456 PHE cc_start: 0.8442 (m-80) cc_final: 0.7642 (m-10) REVERT: B 489 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: B 523 THR cc_start: 0.8614 (p) cc_final: 0.8219 (t) REVERT: B 985 ASP cc_start: 0.7402 (p0) cc_final: 0.6694 (p0) REVERT: B 1146 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7923 (p0) REVERT: C 14 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7198 (pp30) REVERT: C 69 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.4958 (p-80) REVERT: C 170 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: C 342 PHE cc_start: 0.7468 (m-80) cc_final: 0.7233 (m-10) REVERT: C 369 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7577 (p90) REVERT: C 375 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7944 (p90) REVERT: C 515 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8700 (p90) REVERT: C 658 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7749 (p0) REVERT: C 957 GLN cc_start: 0.8156 (tt0) cc_final: 0.7704 (tm-30) REVERT: C 1029 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9159 (tpp) outliers start: 80 outliers final: 18 residues processed: 190 average time/residue: 0.4693 time to fit residues: 110.1714 Evaluate side-chains 127 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 333 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 318 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 104 optimal weight: 0.0770 chunk 304 optimal weight: 0.6980 chunk 187 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C1054 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 = 0.3869 r_free = 0.3869 target = 0.098111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059621 restraints weight = 74103.626| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.68 r_work: 0.2871 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28442 Z= 0.135 Angle : 0.707 17.151 38877 Z= 0.335 Chirality : 0.045 0.282 4637 Planarity : 0.004 0.042 4821 Dihedral : 11.243 108.247 5722 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.47 % Allowed : 13.18 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3327 helix: 1.58 (0.19), residues: 740 sheet: 0.15 (0.18), residues: 721 loop : -1.32 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 646 TYR 0.022 0.001 TYR C1067 PHE 0.020 0.001 PHE C 186 TRP 0.027 0.001 TRP C 152 HIS 0.016 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00293 (28296) covalent geometry : angle 0.67691 (38483) SS BOND : bond 0.00311 ( 44) SS BOND : angle 1.20743 ( 88) hydrogen bonds : bond 0.04270 ( 1086) hydrogen bonds : angle 5.85514 ( 3102) link_ALPHA1-4 : bond 0.01577 ( 18) link_ALPHA1-4 : angle 2.65311 ( 54) link_BETA1-4 : bond 0.00354 ( 30) link_BETA1-4 : angle 1.42772 ( 90) link_BETA1-6 : bond 0.01622 ( 3) link_BETA1-6 : angle 2.03001 ( 9) link_NAG-ASN : bond 0.00403 ( 51) link_NAG-ASN : angle 2.65635 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 105 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8442 (m-80) cc_final: 0.7937 (m-80) REVERT: A 452 LEU cc_start: 0.9009 (tp) cc_final: 0.8799 (tp) REVERT: A 468 ILE cc_start: 0.8085 (pt) cc_final: 0.7860 (mt) REVERT: A 988 GLU cc_start: 0.8658 (mp0) cc_final: 0.8426 (mp0) REVERT: B 176 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5751 (pp) REVERT: B 375 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7273 (p90) REVERT: B 429 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6710 (p90) REVERT: B 646 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8470 (mpp80) REVERT: C 269 TYR cc_start: 0.7166 (m-10) cc_final: 0.6918 (m-10) REVERT: C 375 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8080 (p90) REVERT: C 574 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7716 (p0) REVERT: C 658 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7828 (p0) REVERT: C 957 GLN cc_start: 0.8197 (tt0) cc_final: 0.7693 (tm-30) outliers start: 72 outliers final: 19 residues processed: 166 average time/residue: 0.4525 time to fit residues: 93.8603 Evaluate side-chains 117 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 7 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN C 14 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.096128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.057143 restraints weight = 73849.088| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.63 r_work: 0.2811 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28442 Z= 0.190 Angle : 0.700 16.448 38877 Z= 0.330 Chirality : 0.045 0.239 4637 Planarity : 0.004 0.041 4821 Dihedral : 10.025 106.114 5718 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.64 % Allowed : 13.70 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3327 helix: 1.75 (0.19), residues: 744 sheet: 0.12 (0.18), residues: 763 loop : -1.27 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.021 0.001 TYR C1067 PHE 0.022 0.002 PHE B 486 TRP 0.018 0.001 TRP C 104 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00439 (28296) covalent geometry : angle 0.66555 (38483) SS BOND : bond 0.00411 ( 44) SS BOND : angle 1.41994 ( 88) hydrogen bonds : bond 0.04258 ( 1086) hydrogen bonds : angle 5.66506 ( 3102) link_ALPHA1-4 : bond 0.01690 ( 18) link_ALPHA1-4 : angle 3.32719 ( 54) link_BETA1-4 : bond 0.00260 ( 30) link_BETA1-4 : angle 1.48180 ( 90) link_BETA1-6 : bond 0.01814 ( 3) link_BETA1-6 : angle 2.04484 ( 9) link_NAG-ASN : bond 0.00378 ( 51) link_NAG-ASN : angle 2.51435 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 101 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8486 (m-80) cc_final: 0.7957 (m-80) REVERT: A 468 ILE cc_start: 0.8183 (pt) cc_final: 0.7911 (mt) REVERT: A 988 GLU cc_start: 0.8606 (mp0) cc_final: 0.8316 (mp0) REVERT: B 173 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5745 (tm-30) REVERT: B 465 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: B 634 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6580 (ttp80) REVERT: B 646 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8458 (mpp80) REVERT: B 1050 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8823 (ptm) REVERT: C 269 TYR cc_start: 0.7249 (m-10) cc_final: 0.6969 (m-80) REVERT: C 371 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6143 (p90) REVERT: C 375 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7714 (p90) REVERT: C 658 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8212 (p0) REVERT: C 849 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8222 (tt) outliers start: 77 outliers final: 28 residues processed: 168 average time/residue: 0.4210 time to fit residues: 89.4493 Evaluate side-chains 126 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 285 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 332 optimal weight: 0.3980 chunk 182 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 677 GLN B 907 ASN C 14 GLN C 69 HIS C 580 GLN C 914 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.097091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058293 restraints weight = 73584.374| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.65 r_work: 0.2845 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28442 Z= 0.126 Angle : 0.650 18.367 38877 Z= 0.303 Chirality : 0.044 0.241 4637 Planarity : 0.003 0.041 4821 Dihedral : 9.244 104.871 5715 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.40 % Allowed : 14.79 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3327 helix: 2.04 (0.20), residues: 733 sheet: 0.31 (0.18), residues: 741 loop : -1.18 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.023 0.001 TYR B 170 PHE 0.018 0.001 PHE C 157 TRP 0.021 0.001 TRP C 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00273 (28296) covalent geometry : angle 0.62136 (38483) SS BOND : bond 0.00328 ( 44) SS BOND : angle 1.09113 ( 88) hydrogen bonds : bond 0.03743 ( 1086) hydrogen bonds : angle 5.45266 ( 3102) link_ALPHA1-4 : bond 0.01715 ( 18) link_ALPHA1-4 : angle 2.89814 ( 54) link_BETA1-4 : bond 0.00339 ( 30) link_BETA1-4 : angle 1.35786 ( 90) link_BETA1-6 : bond 0.01814 ( 3) link_BETA1-6 : angle 2.03019 ( 9) link_NAG-ASN : bond 0.00334 ( 51) link_NAG-ASN : angle 2.30218 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 99 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8498 (m-80) cc_final: 0.7999 (m-80) REVERT: A 468 ILE cc_start: 0.8191 (pt) cc_final: 0.7866 (mt) REVERT: A 471 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: A 988 GLU cc_start: 0.8670 (mp0) cc_final: 0.8387 (mp0) REVERT: B 173 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5876 (tm-30) REVERT: B 429 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6468 (p90) REVERT: B 634 ARG cc_start: 0.6932 (ttp80) cc_final: 0.6526 (ttp80) REVERT: B 646 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8430 (mpp80) REVERT: B 1050 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8308 (ppp) REVERT: B 1146 ASP cc_start: 0.8636 (m-30) cc_final: 0.8191 (p0) REVERT: C 269 TYR cc_start: 0.7386 (m-10) cc_final: 0.6960 (m-80) REVERT: C 368 LEU cc_start: 0.9156 (tt) cc_final: 0.8880 (tt) REVERT: C 371 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6092 (p90) REVERT: C 375 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7718 (p90) REVERT: C 658 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8252 (p0) REVERT: C 830 ASP cc_start: 0.7041 (t0) cc_final: 0.6798 (t0) REVERT: C 849 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8191 (tt) outliers start: 70 outliers final: 31 residues processed: 158 average time/residue: 0.4015 time to fit residues: 80.9689 Evaluate side-chains 133 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 310 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 303 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 69 HIS C 677 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.096644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057804 restraints weight = 73745.649| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.65 r_work: 0.2831 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28442 Z= 0.144 Angle : 0.651 18.437 38877 Z= 0.302 Chirality : 0.044 0.235 4637 Planarity : 0.003 0.039 4821 Dihedral : 8.761 103.833 5715 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.64 % Allowed : 14.86 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3327 helix: 2.04 (0.20), residues: 737 sheet: 0.38 (0.19), residues: 721 loop : -1.16 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.021 0.001 TYR C1067 PHE 0.021 0.001 PHE A 338 TRP 0.024 0.001 TRP C 104 HIS 0.012 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00326 (28296) covalent geometry : angle 0.62158 (38483) SS BOND : bond 0.00251 ( 44) SS BOND : angle 1.23719 ( 88) hydrogen bonds : bond 0.03736 ( 1086) hydrogen bonds : angle 5.38484 ( 3102) link_ALPHA1-4 : bond 0.01740 ( 18) link_ALPHA1-4 : angle 2.91167 ( 54) link_BETA1-4 : bond 0.00283 ( 30) link_BETA1-4 : angle 1.38079 ( 90) link_BETA1-6 : bond 0.01777 ( 3) link_BETA1-6 : angle 1.99938 ( 9) link_NAG-ASN : bond 0.00321 ( 51) link_NAG-ASN : angle 2.30273 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 93 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8466 (m-80) cc_final: 0.8169 (m-80) REVERT: A 471 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: A 988 GLU cc_start: 0.8677 (mp0) cc_final: 0.8392 (mp0) REVERT: B 173 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6006 (tm-30) REVERT: B 429 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6555 (p90) REVERT: B 634 ARG cc_start: 0.6903 (ttp80) cc_final: 0.6481 (ttp80) REVERT: B 646 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8456 (mpp80) REVERT: B 1050 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8358 (ppp) REVERT: B 1146 ASP cc_start: 0.8783 (m-30) cc_final: 0.8203 (p0) REVERT: C 269 TYR cc_start: 0.7401 (m-10) cc_final: 0.6930 (m-80) REVERT: C 368 LEU cc_start: 0.9168 (tt) cc_final: 0.8896 (tt) REVERT: C 371 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6028 (p90) REVERT: C 375 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7689 (p90) REVERT: C 658 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8352 (p0) REVERT: C 830 ASP cc_start: 0.7207 (t0) cc_final: 0.6963 (t0) REVERT: C 849 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 912 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.9021 (p) outliers start: 77 outliers final: 36 residues processed: 163 average time/residue: 0.4091 time to fit residues: 84.4534 Evaluate side-chains 133 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 3 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 69 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.093878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.054695 restraints weight = 74073.195| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.65 r_work: 0.2745 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 28442 Z= 0.329 Angle : 0.754 18.199 38877 Z= 0.357 Chirality : 0.047 0.228 4637 Planarity : 0.004 0.040 4821 Dihedral : 8.548 104.031 5715 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 2.88 % Allowed : 14.86 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3327 helix: 1.72 (0.19), residues: 744 sheet: 0.10 (0.18), residues: 741 loop : -1.24 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 646 TYR 0.020 0.002 TYR C1067 PHE 0.025 0.002 PHE A 855 TRP 0.024 0.002 TRP C 104 HIS 0.045 0.002 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00771 (28296) covalent geometry : angle 0.72354 (38483) SS BOND : bond 0.00566 ( 44) SS BOND : angle 1.65967 ( 88) hydrogen bonds : bond 0.04624 ( 1086) hydrogen bonds : angle 5.69313 ( 3102) link_ALPHA1-4 : bond 0.01722 ( 18) link_ALPHA1-4 : angle 2.92775 ( 54) link_BETA1-4 : bond 0.00210 ( 30) link_BETA1-4 : angle 1.58718 ( 90) link_BETA1-6 : bond 0.01724 ( 3) link_BETA1-6 : angle 1.93755 ( 9) link_NAG-ASN : bond 0.00487 ( 51) link_NAG-ASN : angle 2.56071 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 90 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: A 988 GLU cc_start: 0.8635 (mp0) cc_final: 0.8376 (mp0) REVERT: B 173 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6373 (tm-30) REVERT: B 429 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.6486 (p90) REVERT: B 523 THR cc_start: 0.8665 (p) cc_final: 0.8371 (t) REVERT: B 646 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8484 (mpp80) REVERT: B 1050 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8953 (ptm) REVERT: B 1146 ASP cc_start: 0.8845 (m-30) cc_final: 0.8262 (p0) REVERT: C 69 HIS cc_start: 0.6052 (OUTLIER) cc_final: 0.5393 (p-80) REVERT: C 269 TYR cc_start: 0.7204 (m-10) cc_final: 0.6930 (m-10) REVERT: C 309 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8507 (mp0) REVERT: C 368 LEU cc_start: 0.9220 (tt) cc_final: 0.9011 (tt) REVERT: C 371 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6008 (p90) REVERT: C 375 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7790 (p90) outliers start: 84 outliers final: 43 residues processed: 163 average time/residue: 0.4259 time to fit residues: 87.8474 Evaluate side-chains 135 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 84 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1149 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 14 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 327 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 305 optimal weight: 0.0770 chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 330 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 69 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.095848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056863 restraints weight = 73759.533| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.69 r_work: 0.2807 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28442 Z= 0.129 Angle : 0.654 19.686 38877 Z= 0.305 Chirality : 0.043 0.236 4637 Planarity : 0.004 0.039 4821 Dihedral : 8.244 103.245 5714 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 2.19 % Allowed : 15.68 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3327 helix: 1.99 (0.20), residues: 737 sheet: 0.34 (0.19), residues: 710 loop : -1.15 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.021 0.001 TYR C1067 PHE 0.028 0.001 PHE A 855 TRP 0.031 0.001 TRP C 104 HIS 0.027 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00282 (28296) covalent geometry : angle 0.62497 (38483) SS BOND : bond 0.00255 ( 44) SS BOND : angle 1.29763 ( 88) hydrogen bonds : bond 0.03803 ( 1086) hydrogen bonds : angle 5.44470 ( 3102) link_ALPHA1-4 : bond 0.01608 ( 18) link_ALPHA1-4 : angle 2.83859 ( 54) link_BETA1-4 : bond 0.00318 ( 30) link_BETA1-4 : angle 1.35986 ( 90) link_BETA1-6 : bond 0.01821 ( 3) link_BETA1-6 : angle 2.03692 ( 9) link_NAG-ASN : bond 0.00316 ( 51) link_NAG-ASN : angle 2.28197 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 87 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: A 988 GLU cc_start: 0.8697 (mp0) cc_final: 0.8442 (mp0) REVERT: B 173 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: B 429 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.6438 (p90) REVERT: B 465 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: B 634 ARG cc_start: 0.6859 (ttp80) cc_final: 0.6395 (ttp80) REVERT: B 646 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8465 (mpp80) REVERT: B 1050 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.8423 (ppp) REVERT: B 1146 ASP cc_start: 0.8831 (m-30) cc_final: 0.8231 (p0) REVERT: C 269 TYR cc_start: 0.7237 (m-10) cc_final: 0.6786 (m-80) REVERT: C 371 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6055 (p90) REVERT: C 375 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7790 (p90) REVERT: C 830 ASP cc_start: 0.7316 (t0) cc_final: 0.7060 (t0) outliers start: 64 outliers final: 39 residues processed: 144 average time/residue: 0.4417 time to fit residues: 80.4329 Evaluate side-chains 132 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 85 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 114 optimal weight: 3.9990 chunk 326 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 248 optimal weight: 0.4980 chunk 195 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 955 ASN C 69 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.096103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057253 restraints weight = 73687.596| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.67 r_work: 0.2822 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28442 Z= 0.125 Angle : 0.645 19.642 38877 Z= 0.300 Chirality : 0.043 0.230 4637 Planarity : 0.003 0.039 4821 Dihedral : 7.980 101.910 5712 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.88 % Allowed : 16.23 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3327 helix: 2.11 (0.20), residues: 731 sheet: 0.41 (0.19), residues: 701 loop : -1.09 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.021 0.001 TYR C1067 PHE 0.049 0.001 PHE A 855 TRP 0.034 0.001 TRP C 104 HIS 0.024 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00277 (28296) covalent geometry : angle 0.61727 (38483) SS BOND : bond 0.00242 ( 44) SS BOND : angle 1.21653 ( 88) hydrogen bonds : bond 0.03660 ( 1086) hydrogen bonds : angle 5.32779 ( 3102) link_ALPHA1-4 : bond 0.01578 ( 18) link_ALPHA1-4 : angle 2.80945 ( 54) link_BETA1-4 : bond 0.00303 ( 30) link_BETA1-4 : angle 1.34881 ( 90) link_BETA1-6 : bond 0.01893 ( 3) link_BETA1-6 : angle 1.90290 ( 9) link_NAG-ASN : bond 0.00306 ( 51) link_NAG-ASN : angle 2.24100 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 89 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: A 988 GLU cc_start: 0.8688 (mp0) cc_final: 0.8434 (mp0) REVERT: B 173 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: B 429 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6446 (p90) REVERT: B 465 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: B 634 ARG cc_start: 0.6779 (ttp80) cc_final: 0.6345 (ttp80) REVERT: B 646 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8471 (mpp80) REVERT: B 1050 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8345 (ppp) REVERT: B 1146 ASP cc_start: 0.8837 (m-30) cc_final: 0.8242 (p0) REVERT: C 69 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5442 (p-80) REVERT: C 269 TYR cc_start: 0.7241 (m-10) cc_final: 0.6768 (m-80) REVERT: C 371 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6157 (p90) REVERT: C 375 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7790 (p90) REVERT: C 830 ASP cc_start: 0.7325 (t0) cc_final: 0.7067 (t0) outliers start: 55 outliers final: 37 residues processed: 140 average time/residue: 0.4637 time to fit residues: 80.9981 Evaluate side-chains 127 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 297 optimal weight: 0.0270 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.095016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056025 restraints weight = 73824.488| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.64 r_work: 0.2790 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28442 Z= 0.205 Angle : 0.674 19.070 38877 Z= 0.315 Chirality : 0.044 0.243 4637 Planarity : 0.004 0.038 4821 Dihedral : 7.867 101.437 5712 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 1.68 % Allowed : 16.44 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3327 helix: 2.01 (0.20), residues: 737 sheet: 0.35 (0.18), residues: 727 loop : -1.11 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.020 0.001 TYR C1067 PHE 0.029 0.001 PHE B 823 TRP 0.032 0.001 TRP C 104 HIS 0.016 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00475 (28296) covalent geometry : angle 0.64605 (38483) SS BOND : bond 0.00275 ( 44) SS BOND : angle 1.31964 ( 88) hydrogen bonds : bond 0.03932 ( 1086) hydrogen bonds : angle 5.39512 ( 3102) link_ALPHA1-4 : bond 0.01576 ( 18) link_ALPHA1-4 : angle 2.80836 ( 54) link_BETA1-4 : bond 0.00224 ( 30) link_BETA1-4 : angle 1.40094 ( 90) link_BETA1-6 : bond 0.01875 ( 3) link_BETA1-6 : angle 1.50866 ( 9) link_NAG-ASN : bond 0.00329 ( 51) link_NAG-ASN : angle 2.30801 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 90 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: A 988 GLU cc_start: 0.8681 (mp0) cc_final: 0.8429 (mp0) REVERT: B 173 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: B 429 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.6528 (p90) REVERT: B 465 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: B 523 THR cc_start: 0.8570 (p) cc_final: 0.8259 (t) REVERT: B 634 ARG cc_start: 0.6768 (ttp80) cc_final: 0.6315 (ttp80) REVERT: B 646 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8486 (mpp80) REVERT: B 1050 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8464 (ppp) REVERT: B 1146 ASP cc_start: 0.8868 (m-30) cc_final: 0.8265 (p0) REVERT: C 269 TYR cc_start: 0.7268 (m-10) cc_final: 0.6853 (m-80) REVERT: C 371 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6253 (p90) REVERT: C 375 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7786 (p90) REVERT: C 661 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8754 (mp0) REVERT: C 830 ASP cc_start: 0.7382 (t0) cc_final: 0.7134 (t0) outliers start: 49 outliers final: 36 residues processed: 135 average time/residue: 0.4727 time to fit residues: 79.7733 Evaluate side-chains 131 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 153 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 199 optimal weight: 0.0000 chunk 119 optimal weight: 6.9990 chunk 193 optimal weight: 0.0050 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** 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 = 0.3846 r_free = 0.3846 target = 0.096441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057682 restraints weight = 73521.008| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.66 r_work: 0.2830 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28442 Z= 0.115 Angle : 0.638 19.373 38877 Z= 0.297 Chirality : 0.043 0.233 4637 Planarity : 0.003 0.038 4821 Dihedral : 7.664 100.197 5712 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 1.71 % Allowed : 16.51 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3327 helix: 2.16 (0.20), residues: 732 sheet: 0.39 (0.19), residues: 707 loop : -1.06 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.021 0.001 TYR C1067 PHE 0.039 0.001 PHE A 855 TRP 0.037 0.001 TRP C 104 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00249 (28296) covalent geometry : angle 0.61145 (38483) SS BOND : bond 0.00233 ( 44) SS BOND : angle 1.15360 ( 88) hydrogen bonds : bond 0.03519 ( 1086) hydrogen bonds : angle 5.24521 ( 3102) link_ALPHA1-4 : bond 0.01535 ( 18) link_ALPHA1-4 : angle 2.74625 ( 54) link_BETA1-4 : bond 0.00335 ( 30) link_BETA1-4 : angle 1.28551 ( 90) link_BETA1-6 : bond 0.01781 ( 3) link_BETA1-6 : angle 1.36232 ( 9) link_NAG-ASN : bond 0.00313 ( 51) link_NAG-ASN : angle 2.18400 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8259.22 seconds wall clock time: 141 minutes 37.74 seconds (8497.74 seconds total)