Starting phenix.real_space_refine on Fri Mar 6 06:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx7_30898/03_2026/7dx7_30898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx7_30898/03_2026/7dx7_30898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dx7_30898/03_2026/7dx7_30898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx7_30898/03_2026/7dx7_30898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx7_30898/03_2026/7dx7_30898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx7_30898/03_2026/7dx7_30898.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 133 5.16 5 C 18475 2.51 5 N 4720 2.21 5 O 5717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29045 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" 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: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.76, per 1000 atoms: 0.23 Number of scatterers: 29045 At special positions: 0 Unit cell: (135.875, 194.573, 205.443, 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 133 16.00 O 5717 8.00 N 4720 7.00 C 18475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.17 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=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.52 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.31 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.10 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.48 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.13 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=2.06 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.43 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 BETA1-4 " NAG B1409 " - " NAG B1410 " " 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN D 90 " " NAG c 1 " - " ASN D 103 " " NAG d 1 " - " ASN D 432 " " NAG e 1 " - " ASN D 546 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6658 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 45 sheets defined 31.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.739A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 4.064A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.792A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.756A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.688A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.527A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.550A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.308A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.759A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.549A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.678A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.592A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.395A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.578A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.983A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.544A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.851A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 316 removed outlier: 6.515A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC5, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.344A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.699A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.661A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.031A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.583A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3018 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: 6.23 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6580 1.33 - 1.45: 7437 1.45 - 1.58: 15494 1.58 - 1.70: 0 1.70 - 1.83: 181 Bond restraints: 29692 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.30e+01 bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.79e+01 bond pdb=" N PRO B 337 " pdb=" CD PRO B 337 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 ... (remaining 29687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 39321 2.66 - 5.32: 964 5.32 - 7.99: 77 7.99 - 10.65: 10 10.65 - 13.31: 6 Bond angle restraints: 40378 Sorted by residual: angle pdb=" N CYS C 538 " pdb=" CA CYS C 538 " pdb=" C CYS C 538 " ideal model delta sigma weight residual 110.10 100.85 9.25 1.49e+00 4.50e-01 3.85e+01 angle pdb=" N CYS B 538 " pdb=" CA CYS B 538 " pdb=" C CYS B 538 " ideal model delta sigma weight residual 110.10 100.91 9.19 1.49e+00 4.50e-01 3.81e+01 angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.34 -9.58 1.59e+00 3.96e-01 3.63e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 ... (remaining 40373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16183 17.95 - 35.90: 1732 35.90 - 53.84: 581 53.84 - 71.79: 188 71.79 - 89.74: 52 Dihedral angle restraints: 18736 sinusoidal: 8408 harmonic: 10328 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 179.36 -86.36 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -8.00 -78.00 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 18733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4766 0.329 - 0.657: 5 0.657 - 0.986: 5 0.986 - 1.315: 0 1.315 - 1.644: 1 Chirality restraints: 4777 Sorted by residual: chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 4774 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG c 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.14e+02 pdb=" C7 NAG c 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " 0.048 2.00e-02 2.50e+03 9.65e-02 1.16e+02 pdb=" CG ASN D 103 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.173 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " 0.108 2.00e-02 2.50e+03 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 233 2.50 - 3.10: 20353 3.10 - 3.70: 41327 3.70 - 4.30: 63080 4.30 - 4.90: 104411 Nonbonded interactions: 229404 Sorted by model distance: nonbonded pdb=" O PHE B 559 " pdb=" O LEU B 560 " model vdw 1.897 3.040 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" O ASN A 334 " pdb=" ND2 ASN A 334 " model vdw 1.968 3.120 nonbonded pdb=" O VAL B 534 " pdb=" CG LYS B 535 " model vdw 1.978 3.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.981 3.120 ... (remaining 229399 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 27 through 455 or resid 491 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and resid 27 through 1408) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.220 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.491 29814 Z= 0.559 Angle : 1.307 71.298 40704 Z= 0.680 Chirality : 0.073 1.644 4777 Planarity : 0.009 0.305 5112 Dihedral : 17.542 89.741 11958 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.62 % Favored : 87.94 % Rotamer: Outliers : 11.04 % Allowed : 16.03 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.38 (0.11), residues: 3484 helix: -2.94 (0.12), residues: 991 sheet: -1.94 (0.17), residues: 706 loop : -3.35 (0.11), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP B 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01125 (29692) covalent geometry : angle 1.00979 (40378) SS BOND : bond 0.13777 ( 40) SS BOND : angle 14.48757 ( 80) hydrogen bonds : bond 0.22638 ( 1062) hydrogen bonds : angle 8.11555 ( 3018) link_BETA1-4 : bond 0.03753 ( 28) link_BETA1-4 : angle 4.22750 ( 84) link_NAG-ASN : bond 0.02453 ( 54) link_NAG-ASN : angle 7.88109 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 343 poor density : 576 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 THR cc_start: 0.4791 (OUTLIER) cc_final: 0.4570 (p) REVERT: A 590 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6596 (m) REVERT: A 696 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 100 ILE cc_start: 0.8868 (mm) cc_final: 0.8507 (mt) REVERT: B 153 MET cc_start: 0.0516 (mpp) cc_final: -0.3079 (tmm) REVERT: B 164 ASN cc_start: 0.4727 (OUTLIER) cc_final: 0.3671 (m-40) REVERT: B 519 HIS cc_start: 0.2283 (OUTLIER) cc_final: 0.1890 (m170) REVERT: B 935 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: B 974 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7373 (t) REVERT: C 81 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.6361 (m-40) REVERT: C 384 PRO cc_start: 0.6657 (Cg_exo) cc_final: 0.6443 (Cg_endo) REVERT: C 389 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6464 (p0) REVERT: C 500 THR cc_start: 0.3716 (OUTLIER) cc_final: 0.3479 (m) REVERT: C 535 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6073 (mttp) REVERT: C 562 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.5827 (p90) REVERT: C 567 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6102 (ptp-170) REVERT: D 82 MET cc_start: 0.4032 (mmt) cc_final: 0.3443 (tpp) REVERT: D 225 ASP cc_start: 0.5001 (m-30) cc_final: 0.3014 (t0) REVERT: D 285 PHE cc_start: 0.0902 (m-80) cc_final: 0.0301 (m-80) REVERT: D 309 LYS cc_start: 0.6436 (mmtt) cc_final: 0.5442 (mttp) REVERT: D 344 CYS cc_start: 0.2666 (OUTLIER) cc_final: 0.1707 (m) REVERT: D 423 LEU cc_start: -0.0500 (OUTLIER) cc_final: -0.0704 (tp) REVERT: D 517 THR cc_start: 0.5863 (p) cc_final: 0.4650 (t) REVERT: D 591 LEU cc_start: 0.1679 (tp) cc_final: 0.1439 (tp) outliers start: 343 outliers final: 87 residues processed: 852 average time/residue: 0.1863 time to fit residues: 251.4396 Evaluate side-chains 364 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 262 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 423 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN A 188 ASN A 440 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 764 ASN A 901 GLN A 913 GLN A 914 ASN A 919 ASN A 926 GLN A 969 ASN A 992 GLN A1058 HIS A1101 HIS B 115 GLN B 137 ASN B 188 ASN B 239 GLN B 245 HIS B 360 ASN B 422 ASN B 440 ASN B 498 GLN B 644 GLN B 655 HIS B 762 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1054 GLN C 115 GLN C 134 GLN C 137 ASN C 188 ASN C 360 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 498 GLN C 564 GLN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 992 GLN C1005 GLN C1010 GLN C1071 GLN C1101 HIS D 58 ASN D 96 GLN D 175 GLN D 277 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.176758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130648 restraints weight = 53444.987| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.62 r_work: 0.3322 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29814 Z= 0.159 Angle : 0.810 14.780 40704 Z= 0.398 Chirality : 0.050 0.467 4777 Planarity : 0.006 0.068 5112 Dihedral : 10.069 59.924 5666 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.66 % Favored : 92.08 % Rotamer: Outliers : 5.25 % Allowed : 18.60 % Favored : 76.15 % Cbeta Deviations : 0.03 % 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: -2.71 (0.13), residues: 3484 helix: -0.62 (0.16), residues: 991 sheet: -1.29 (0.19), residues: 688 loop : -2.77 (0.12), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 509 TYR 0.031 0.002 TYR A 505 PHE 0.027 0.002 PHE D 72 TRP 0.035 0.002 TRP D 349 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00343 (29692) covalent geometry : angle 0.77441 (40378) SS BOND : bond 0.00544 ( 40) SS BOND : angle 2.26201 ( 80) hydrogen bonds : bond 0.05357 ( 1062) hydrogen bonds : angle 5.63159 ( 3018) link_BETA1-4 : bond 0.00700 ( 28) link_BETA1-4 : angle 2.38835 ( 84) link_NAG-ASN : bond 0.00479 ( 54) link_NAG-ASN : angle 3.14251 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 303 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6814 (mt0) cc_final: 0.6430 (mm-40) REVERT: A 122 ASN cc_start: 0.4965 (OUTLIER) cc_final: 0.4141 (m110) REVERT: A 364 ASP cc_start: 0.8193 (p0) cc_final: 0.7979 (p0) REVERT: A 399 SER cc_start: 0.7237 (OUTLIER) cc_final: 0.6758 (p) REVERT: A 556 ASN cc_start: 0.8494 (p0) cc_final: 0.8287 (p0) REVERT: A 696 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 740 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8036 (ttt) REVERT: A 747 THR cc_start: 0.8568 (m) cc_final: 0.8141 (p) REVERT: B 100 ILE cc_start: 0.9018 (mm) cc_final: 0.8735 (mt) REVERT: B 153 MET cc_start: 0.0161 (mpp) cc_final: -0.3352 (tmm) REVERT: B 324 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.4899 (mm-30) REVERT: B 356 LYS cc_start: 0.2938 (tttp) cc_final: 0.2726 (tttp) REVERT: B 357 ARG cc_start: 0.6348 (tmm160) cc_final: 0.6113 (tmm160) REVERT: B 558 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6088 (tmtt) REVERT: B 697 MET cc_start: 0.8961 (ptm) cc_final: 0.8743 (ptp) REVERT: B 902 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8873 (mmt) REVERT: C 48 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 95 THR cc_start: 0.8123 (p) cc_final: 0.7875 (p) REVERT: C 153 MET cc_start: 0.2450 (mpp) cc_final: 0.2008 (mpp) REVERT: C 187 LYS cc_start: 0.4409 (mtmm) cc_final: 0.3802 (mmtp) REVERT: C 336 CYS cc_start: 0.5753 (OUTLIER) cc_final: 0.4461 (m) REVERT: C 347 PHE cc_start: 0.4947 (m-80) cc_final: 0.4617 (m-80) REVERT: C 387 LEU cc_start: 0.7100 (mt) cc_final: 0.6821 (mt) REVERT: C 389 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6285 (p0) REVERT: C 417 LYS cc_start: 0.4020 (OUTLIER) cc_final: 0.2968 (ttpt) REVERT: C 567 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6884 (ptp-170) REVERT: D 73 LEU cc_start: 0.7562 (tt) cc_final: 0.7242 (mt) REVERT: D 79 LEU cc_start: 0.7023 (mt) cc_final: 0.6442 (tt) REVERT: D 82 MET cc_start: 0.4487 (mmt) cc_final: 0.3880 (tpp) REVERT: D 94 LYS cc_start: 0.4517 (OUTLIER) cc_final: 0.4196 (mtmm) REVERT: D 102 GLN cc_start: 0.4506 (pp30) cc_final: 0.3547 (mm110) REVERT: D 270 MET cc_start: 0.1512 (mmm) cc_final: 0.1035 (mtp) REVERT: D 285 PHE cc_start: 0.3178 (m-80) cc_final: 0.2342 (m-80) REVERT: D 309 LYS cc_start: 0.7517 (mmtt) cc_final: 0.6806 (mttt) REVERT: D 344 CYS cc_start: 0.1797 (OUTLIER) cc_final: 0.0834 (t) REVERT: D 366 MET cc_start: 0.5964 (tmm) cc_final: 0.5692 (tpp) REVERT: D 455 MET cc_start: 0.1686 (ppp) cc_final: 0.1185 (ptt) REVERT: D 591 LEU cc_start: 0.2087 (tp) cc_final: 0.1662 (tp) outliers start: 163 outliers final: 79 residues processed: 439 average time/residue: 0.1777 time to fit residues: 127.0174 Evaluate side-chains 328 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 235 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 307 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 148 optimal weight: 0.0970 chunk 124 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 703 ASN A 804 GLN A 913 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 658 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.170885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121816 restraints weight = 53372.664| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.75 r_work: 0.3196 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 29814 Z= 0.233 Angle : 0.818 17.173 40704 Z= 0.394 Chirality : 0.052 0.395 4777 Planarity : 0.005 0.067 5112 Dihedral : 8.951 59.448 5583 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.92 % Favored : 91.93 % Rotamer: Outliers : 5.21 % Allowed : 19.57 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 3484 helix: 0.21 (0.17), residues: 978 sheet: -0.98 (0.18), residues: 714 loop : -2.41 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 44 TYR 0.026 0.002 TYR D 199 PHE 0.023 0.002 PHE A 86 TRP 0.030 0.002 TRP D 477 HIS 0.009 0.002 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00560 (29692) covalent geometry : angle 0.78223 (40378) SS BOND : bond 0.00653 ( 40) SS BOND : angle 2.39175 ( 80) hydrogen bonds : bond 0.05195 ( 1062) hydrogen bonds : angle 5.46993 ( 3018) link_BETA1-4 : bond 0.00575 ( 28) link_BETA1-4 : angle 2.36391 ( 84) link_NAG-ASN : bond 0.00503 ( 54) link_NAG-ASN : angle 3.17489 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 261 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7067 (mt0) cc_final: 0.6557 (mm-40) REVERT: A 364 ASP cc_start: 0.8521 (p0) cc_final: 0.8207 (p0) REVERT: A 399 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6745 (p) REVERT: A 515 PHE cc_start: 0.7516 (m-80) cc_final: 0.7276 (m-80) REVERT: B 141 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6962 (pt) REVERT: B 153 MET cc_start: 0.0710 (mpp) cc_final: -0.3439 (tmm) REVERT: B 321 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7599 (mm-40) REVERT: B 356 LYS cc_start: 0.2633 (tttp) cc_final: 0.2377 (tttp) REVERT: B 390 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5854 (tt) REVERT: B 558 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.5971 (tmtt) REVERT: B 878 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 936 ASP cc_start: 0.8428 (m-30) cc_final: 0.8164 (m-30) REVERT: B 979 ASP cc_start: 0.7742 (m-30) cc_final: 0.7533 (m-30) REVERT: C 48 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 216 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5631 (tt) REVERT: C 347 PHE cc_start: 0.5419 (m-80) cc_final: 0.4822 (m-80) REVERT: C 389 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6511 (p0) REVERT: C 417 LYS cc_start: 0.3924 (OUTLIER) cc_final: 0.2746 (ttpt) REVERT: C 1132 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9133 (pp) REVERT: D 28 PHE cc_start: 0.4681 (t80) cc_final: 0.4465 (t80) REVERT: D 49 ASN cc_start: 0.6981 (m-40) cc_final: 0.6663 (t0) REVERT: D 79 LEU cc_start: 0.7302 (mt) cc_final: 0.7006 (tp) REVERT: D 115 ARG cc_start: 0.4525 (tpt170) cc_final: 0.4159 (tpp-160) REVERT: D 123 MET cc_start: 0.2269 (mtp) cc_final: 0.1991 (mtt) REVERT: D 224 GLU cc_start: 0.7255 (mp0) cc_final: 0.6859 (mp0) REVERT: D 270 MET cc_start: 0.0994 (mmm) cc_final: 0.0690 (mtp) REVERT: D 285 PHE cc_start: 0.2541 (m-80) cc_final: 0.1501 (m-80) REVERT: D 309 LYS cc_start: 0.7564 (mmtt) cc_final: 0.6761 (mttp) REVERT: D 579 MET cc_start: 0.3213 (mtp) cc_final: 0.2690 (mtm) outliers start: 162 outliers final: 106 residues processed: 404 average time/residue: 0.1614 time to fit residues: 110.0844 Evaluate side-chains 319 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 203 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 293 optimal weight: 0.0980 chunk 117 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 256 optimal weight: 0.0670 chunk 299 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 992 GLN B1010 GLN C 81 ASN C 422 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.173279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125325 restraints weight = 53183.201| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.56 r_work: 0.3258 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29814 Z= 0.119 Angle : 0.685 16.794 40704 Z= 0.326 Chirality : 0.048 0.469 4777 Planarity : 0.004 0.051 5112 Dihedral : 7.963 59.742 5565 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 3.70 % Allowed : 21.63 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3484 helix: 0.64 (0.17), residues: 974 sheet: -0.67 (0.18), residues: 748 loop : -2.18 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.019 0.001 TYR D 199 PHE 0.022 0.001 PHE D 592 TRP 0.025 0.001 TRP D 477 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00262 (29692) covalent geometry : angle 0.64539 (40378) SS BOND : bond 0.00400 ( 40) SS BOND : angle 1.79496 ( 80) hydrogen bonds : bond 0.03820 ( 1062) hydrogen bonds : angle 5.09299 ( 3018) link_BETA1-4 : bond 0.00798 ( 28) link_BETA1-4 : angle 2.31790 ( 84) link_NAG-ASN : bond 0.00407 ( 54) link_NAG-ASN : angle 3.11942 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 243 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6902 (mt0) cc_final: 0.6394 (mm-40) REVERT: A 191 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 226 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7687 (tp) REVERT: A 399 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.7048 (p) REVERT: A 515 PHE cc_start: 0.7432 (m-80) cc_final: 0.7186 (m-80) REVERT: A 531 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7279 (p) REVERT: A 696 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 916 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9226 (tp) REVERT: A 995 ARG cc_start: 0.8333 (mtt90) cc_final: 0.8126 (mtm180) REVERT: B 141 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7007 (pt) REVERT: B 153 MET cc_start: 0.0635 (mpp) cc_final: -0.3433 (tmm) REVERT: B 160 TYR cc_start: 0.7396 (p90) cc_final: 0.7005 (p90) REVERT: B 390 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5946 (tt) REVERT: B 518 LEU cc_start: 0.0160 (OUTLIER) cc_final: -0.0051 (tt) REVERT: B 558 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6349 (tmtt) REVERT: B 878 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 936 ASP cc_start: 0.8252 (m-30) cc_final: 0.7995 (m-30) REVERT: B 983 ARG cc_start: 0.8125 (ptm160) cc_final: 0.7676 (ptm160) REVERT: C 48 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8294 (mt) REVERT: C 153 MET cc_start: 0.2201 (mpp) cc_final: 0.1792 (mpp) REVERT: C 336 CYS cc_start: 0.5327 (OUTLIER) cc_final: 0.4214 (m) REVERT: C 347 PHE cc_start: 0.5503 (m-80) cc_final: 0.4941 (m-80) REVERT: C 389 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6510 (p0) REVERT: C 417 LYS cc_start: 0.3616 (OUTLIER) cc_final: 0.2332 (tmmt) REVERT: C 740 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8614 (ttm) REVERT: C 1029 MET cc_start: 0.9111 (tpp) cc_final: 0.8823 (ttm) REVERT: C 1132 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9100 (pp) REVERT: D 28 PHE cc_start: 0.4842 (t80) cc_final: 0.4568 (t80) REVERT: D 49 ASN cc_start: 0.6984 (m-40) cc_final: 0.6690 (t0) REVERT: D 73 LEU cc_start: 0.7206 (tp) cc_final: 0.6935 (mm) REVERT: D 79 LEU cc_start: 0.7246 (mt) cc_final: 0.6749 (tt) REVERT: D 115 ARG cc_start: 0.4510 (tpt170) cc_final: 0.4306 (tpp-160) REVERT: D 270 MET cc_start: 0.1036 (mmm) cc_final: 0.0533 (mtp) REVERT: D 309 LYS cc_start: 0.7590 (mmtt) cc_final: 0.6826 (mttp) REVERT: D 517 THR cc_start: 0.5427 (p) cc_final: 0.5189 (p) outliers start: 115 outliers final: 66 residues processed: 341 average time/residue: 0.1592 time to fit residues: 91.1796 Evaluate side-chains 290 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 208 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 189 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 294 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 334 ASN B 450 ASN C 957 GLN C1106 GLN D 81 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.169623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123541 restraints weight = 53037.473| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.61 r_work: 0.3210 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29814 Z= 0.218 Angle : 0.743 13.607 40704 Z= 0.357 Chirality : 0.050 0.450 4777 Planarity : 0.004 0.056 5112 Dihedral : 7.799 59.731 5558 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 4.44 % Allowed : 21.27 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3484 helix: 0.70 (0.17), residues: 993 sheet: -0.66 (0.18), residues: 748 loop : -2.13 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.027 0.002 TYR D 199 PHE 0.021 0.002 PHE A 86 TRP 0.013 0.002 TRP D 473 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00525 (29692) covalent geometry : angle 0.71016 (40378) SS BOND : bond 0.00464 ( 40) SS BOND : angle 2.06026 ( 80) hydrogen bonds : bond 0.04592 ( 1062) hydrogen bonds : angle 5.23909 ( 3018) link_BETA1-4 : bond 0.00879 ( 28) link_BETA1-4 : angle 2.37229 ( 84) link_NAG-ASN : bond 0.00367 ( 54) link_NAG-ASN : angle 2.81527 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 229 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6668 (m90) REVERT: A 115 GLN cc_start: 0.6896 (mt0) cc_final: 0.6436 (mm-40) REVERT: A 226 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7604 (tp) REVERT: A 281 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: A 399 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7137 (p) REVERT: A 441 LEU cc_start: 0.7532 (mm) cc_final: 0.7229 (mm) REVERT: A 515 PHE cc_start: 0.7522 (m-80) cc_final: 0.7152 (m-80) REVERT: A 531 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7243 (p) REVERT: B 111 ASP cc_start: 0.5214 (OUTLIER) cc_final: 0.4641 (m-30) REVERT: B 153 MET cc_start: 0.0457 (mpp) cc_final: -0.3760 (tmm) REVERT: B 160 TYR cc_start: 0.7448 (p90) cc_final: 0.7102 (p90) REVERT: B 390 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6108 (tt) REVERT: B 558 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6566 (tmtt) REVERT: C 48 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8297 (mt) REVERT: C 216 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5515 (tt) REVERT: C 336 CYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4161 (m) REVERT: C 347 PHE cc_start: 0.5563 (m-80) cc_final: 0.5089 (m-80) REVERT: C 387 LEU cc_start: 0.7005 (mt) cc_final: 0.6797 (tp) REVERT: C 389 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6645 (p0) REVERT: C 417 LYS cc_start: 0.4273 (OUTLIER) cc_final: 0.2867 (tmmt) REVERT: C 1132 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9159 (pp) REVERT: D 28 PHE cc_start: 0.4864 (t80) cc_final: 0.4652 (t80) REVERT: D 73 LEU cc_start: 0.7176 (tp) cc_final: 0.6929 (mm) REVERT: D 79 LEU cc_start: 0.7389 (mt) cc_final: 0.6896 (tt) REVERT: D 81 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5995 (tm-30) REVERT: D 115 ARG cc_start: 0.4704 (tpt170) cc_final: 0.4360 (tpp-160) REVERT: D 123 MET cc_start: 0.2208 (mtp) cc_final: 0.1995 (mtt) REVERT: D 270 MET cc_start: 0.1404 (mmm) cc_final: 0.0714 (mtp) REVERT: D 309 LYS cc_start: 0.7623 (mmtt) cc_final: 0.6841 (mttt) REVERT: D 344 CYS cc_start: 0.1993 (OUTLIER) cc_final: 0.0984 (t) REVERT: D 484 ILE cc_start: 0.2930 (mt) cc_final: 0.2550 (mm) REVERT: D 517 THR cc_start: 0.5696 (p) cc_final: 0.5441 (p) outliers start: 138 outliers final: 93 residues processed: 352 average time/residue: 0.1563 time to fit residues: 93.8630 Evaluate side-chains 315 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 206 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 562 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 202 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 90 optimal weight: 0.0980 chunk 236 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 221 optimal weight: 40.0000 chunk 272 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 913 GLN D 81 GLN ** D 388 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 = 0.4240 r_free = 0.4240 target = 0.171502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124960 restraints weight = 53066.076| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.64 r_work: 0.3249 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29814 Z= 0.120 Angle : 0.661 13.138 40704 Z= 0.315 Chirality : 0.047 0.481 4777 Planarity : 0.004 0.046 5112 Dihedral : 7.295 59.013 5552 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 3.73 % Allowed : 22.18 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3484 helix: 0.96 (0.17), residues: 989 sheet: -0.48 (0.18), residues: 744 loop : -2.02 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.021 0.001 TYR D 202 PHE 0.021 0.001 PHE C 541 TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00267 (29692) covalent geometry : angle 0.63118 (40378) SS BOND : bond 0.00417 ( 40) SS BOND : angle 1.71775 ( 80) hydrogen bonds : bond 0.03751 ( 1062) hydrogen bonds : angle 4.98868 ( 3018) link_BETA1-4 : bond 0.00636 ( 28) link_BETA1-4 : angle 2.23825 ( 84) link_NAG-ASN : bond 0.00331 ( 54) link_NAG-ASN : angle 2.51942 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 220 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6927 (mt0) cc_final: 0.6495 (mm-40) REVERT: A 281 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: A 399 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7449 (p) REVERT: A 515 PHE cc_start: 0.7329 (m-80) cc_final: 0.7007 (m-80) REVERT: A 531 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7212 (p) REVERT: A 696 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8634 (p) REVERT: A 747 THR cc_start: 0.8886 (m) cc_final: 0.8548 (p) REVERT: B 141 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6972 (pt) REVERT: B 153 MET cc_start: 0.0491 (mpp) cc_final: -0.3693 (tmm) REVERT: B 160 TYR cc_start: 0.7361 (p90) cc_final: 0.7102 (p90) REVERT: B 390 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6104 (tt) REVERT: B 558 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6472 (tmtt) REVERT: C 48 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8279 (mt) REVERT: C 216 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5379 (tt) REVERT: C 336 CYS cc_start: 0.5246 (OUTLIER) cc_final: 0.4136 (m) REVERT: C 347 PHE cc_start: 0.5508 (m-80) cc_final: 0.5063 (m-80) REVERT: C 417 LYS cc_start: 0.4245 (OUTLIER) cc_final: 0.2872 (tmmt) REVERT: C 740 MET cc_start: 0.8874 (ttp) cc_final: 0.8670 (ttm) REVERT: C 1132 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9099 (pp) REVERT: D 28 PHE cc_start: 0.5178 (t80) cc_final: 0.4935 (t80) REVERT: D 73 LEU cc_start: 0.7292 (tp) cc_final: 0.7067 (mm) REVERT: D 79 LEU cc_start: 0.7390 (mt) cc_final: 0.6822 (tt) REVERT: D 115 ARG cc_start: 0.4566 (tpt170) cc_final: 0.4355 (tpp-160) REVERT: D 123 MET cc_start: 0.2218 (mtp) cc_final: 0.1983 (mtt) REVERT: D 236 LEU cc_start: 0.4362 (mt) cc_final: 0.3979 (pp) REVERT: D 270 MET cc_start: 0.1335 (mmm) cc_final: 0.0681 (mtp) REVERT: D 309 LYS cc_start: 0.7606 (mmtt) cc_final: 0.6886 (mttt) REVERT: D 335 ASP cc_start: 0.3591 (p0) cc_final: 0.3226 (t0) REVERT: D 344 CYS cc_start: 0.1919 (OUTLIER) cc_final: 0.0939 (t) REVERT: D 517 THR cc_start: 0.5655 (p) cc_final: 0.5156 (p) REVERT: D 591 LEU cc_start: 0.1287 (tt) cc_final: 0.0735 (pp) outliers start: 116 outliers final: 70 residues processed: 324 average time/residue: 0.1647 time to fit residues: 89.9890 Evaluate side-chains 289 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 206 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 76 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 339 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 325 optimal weight: 0.0980 chunk 264 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 234 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1071 GLN B 613 GLN B1071 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.172569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126032 restraints weight = 53063.522| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.52 r_work: 0.3274 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29814 Z= 0.108 Angle : 0.635 12.453 40704 Z= 0.302 Chirality : 0.047 0.554 4777 Planarity : 0.004 0.047 5112 Dihedral : 6.843 58.778 5543 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 3.67 % Allowed : 22.21 % Favored : 74.12 % 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: -0.94 (0.14), residues: 3484 helix: 1.20 (0.17), residues: 983 sheet: -0.34 (0.19), residues: 745 loop : -1.90 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.019 0.001 TYR A 449 PHE 0.024 0.001 PHE D 285 TRP 0.016 0.001 TRP D 203 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00236 (29692) covalent geometry : angle 0.60874 (40378) SS BOND : bond 0.00327 ( 40) SS BOND : angle 1.51118 ( 80) hydrogen bonds : bond 0.03379 ( 1062) hydrogen bonds : angle 4.80716 ( 3018) link_BETA1-4 : bond 0.00651 ( 28) link_BETA1-4 : angle 2.14293 ( 84) link_NAG-ASN : bond 0.00326 ( 54) link_NAG-ASN : angle 2.33871 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 227 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.6145 (m-70) REVERT: A 115 GLN cc_start: 0.6930 (mt0) cc_final: 0.6445 (mm-40) REVERT: A 226 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 390 LEU cc_start: 0.6016 (mp) cc_final: 0.5624 (mt) REVERT: A 515 PHE cc_start: 0.7334 (m-80) cc_final: 0.6954 (m-80) REVERT: A 531 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 696 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 747 THR cc_start: 0.8863 (m) cc_final: 0.8549 (p) REVERT: A 916 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9152 (tp) REVERT: A 983 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7187 (ptm160) REVERT: B 137 ASN cc_start: 0.7419 (m-40) cc_final: 0.6484 (t0) REVERT: B 153 MET cc_start: 0.0458 (mpp) cc_final: -0.3646 (tmm) REVERT: B 390 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6205 (tt) REVERT: B 558 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6461 (tmtt) REVERT: B 794 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7651 (pp) REVERT: C 347 PHE cc_start: 0.5308 (m-80) cc_final: 0.4936 (m-80) REVERT: C 417 LYS cc_start: 0.4014 (OUTLIER) cc_final: 0.2691 (tmmt) REVERT: C 740 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8588 (ttm) REVERT: C 1029 MET cc_start: 0.9041 (tpp) cc_final: 0.8784 (ttm) REVERT: C 1132 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9098 (pp) REVERT: D 28 PHE cc_start: 0.5264 (t80) cc_final: 0.5040 (t80) REVERT: D 73 LEU cc_start: 0.7335 (tp) cc_final: 0.7110 (mm) REVERT: D 79 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6811 (tt) REVERT: D 100 LEU cc_start: 0.7524 (tp) cc_final: 0.7289 (pp) REVERT: D 115 ARG cc_start: 0.4532 (tpt170) cc_final: 0.4323 (tpp-160) REVERT: D 123 MET cc_start: 0.2264 (mtp) cc_final: 0.2013 (mtt) REVERT: D 236 LEU cc_start: 0.4398 (mt) cc_final: 0.3926 (pp) REVERT: D 270 MET cc_start: 0.0979 (mmm) cc_final: 0.0523 (mtp) REVERT: D 309 LYS cc_start: 0.7618 (mmtt) cc_final: 0.6893 (mttp) REVERT: D 335 ASP cc_start: 0.3602 (p0) cc_final: 0.3243 (t0) REVERT: D 344 CYS cc_start: 0.1572 (OUTLIER) cc_final: 0.0590 (t) REVERT: D 470 LYS cc_start: 0.2838 (mttm) cc_final: 0.2092 (mtpt) REVERT: D 568 LEU cc_start: 0.4309 (tt) cc_final: 0.3919 (mp) REVERT: D 591 LEU cc_start: 0.1307 (OUTLIER) cc_final: 0.0754 (pp) outliers start: 114 outliers final: 73 residues processed: 323 average time/residue: 0.1572 time to fit residues: 86.0902 Evaluate side-chains 296 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 208 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 591 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 188 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 347 optimal weight: 7.9990 chunk 68 optimal weight: 0.0060 chunk 225 optimal weight: 0.7980 chunk 348 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 341 optimal weight: 2.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.171866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126555 restraints weight = 52912.824| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.54 r_work: 0.3265 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29814 Z= 0.125 Angle : 0.650 12.043 40704 Z= 0.310 Chirality : 0.047 0.482 4777 Planarity : 0.004 0.048 5112 Dihedral : 6.741 59.964 5537 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 3.32 % Allowed : 22.66 % Favored : 74.03 % 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: -0.85 (0.14), residues: 3484 helix: 1.30 (0.17), residues: 981 sheet: -0.32 (0.19), residues: 758 loop : -1.84 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 158 TYR 0.023 0.001 TYR A 473 PHE 0.030 0.001 PHE A 65 TRP 0.011 0.001 TRP D 203 HIS 0.024 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00291 (29692) covalent geometry : angle 0.62501 (40378) SS BOND : bond 0.00368 ( 40) SS BOND : angle 1.72464 ( 80) hydrogen bonds : bond 0.03493 ( 1062) hydrogen bonds : angle 4.79177 ( 3018) link_BETA1-4 : bond 0.00622 ( 28) link_BETA1-4 : angle 2.11556 ( 84) link_NAG-ASN : bond 0.00319 ( 54) link_NAG-ASN : angle 2.26832 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 219 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6877 (mt0) cc_final: 0.6451 (mm-40) REVERT: A 200 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: A 390 LEU cc_start: 0.5947 (mp) cc_final: 0.5513 (mt) REVERT: A 515 PHE cc_start: 0.7333 (m-80) cc_final: 0.6955 (m-80) REVERT: A 531 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7263 (p) REVERT: A 696 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 747 THR cc_start: 0.8825 (m) cc_final: 0.8535 (p) REVERT: A 983 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7219 (ptm160) REVERT: B 137 ASN cc_start: 0.7247 (m-40) cc_final: 0.6365 (t0) REVERT: B 153 MET cc_start: 0.0423 (mpp) cc_final: -0.3648 (tmm) REVERT: B 390 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6174 (tt) REVERT: B 558 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6492 (tmtt) REVERT: B 794 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7607 (pp) REVERT: B 936 ASP cc_start: 0.8135 (m-30) cc_final: 0.7898 (m-30) REVERT: C 216 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5329 (tt) REVERT: C 347 PHE cc_start: 0.5312 (m-80) cc_final: 0.4941 (m-80) REVERT: C 417 LYS cc_start: 0.4138 (OUTLIER) cc_final: 0.2832 (tmmt) REVERT: C 740 MET cc_start: 0.8833 (ttp) cc_final: 0.8621 (ttm) REVERT: C 1029 MET cc_start: 0.9064 (tpp) cc_final: 0.8806 (ttm) REVERT: C 1132 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9103 (pp) REVERT: D 28 PHE cc_start: 0.5195 (t80) cc_final: 0.4978 (t80) REVERT: D 79 LEU cc_start: 0.7381 (mt) cc_final: 0.6856 (tt) REVERT: D 100 LEU cc_start: 0.7517 (tp) cc_final: 0.7262 (pp) REVERT: D 115 ARG cc_start: 0.4580 (tpt170) cc_final: 0.4375 (tpp-160) REVERT: D 236 LEU cc_start: 0.4421 (mt) cc_final: 0.3940 (pp) REVERT: D 270 MET cc_start: 0.1237 (mmm) cc_final: 0.0856 (mtp) REVERT: D 309 LYS cc_start: 0.7618 (mmtt) cc_final: 0.6890 (mttp) REVERT: D 344 CYS cc_start: 0.1590 (OUTLIER) cc_final: 0.0631 (t) REVERT: D 470 LYS cc_start: 0.2778 (mttm) cc_final: 0.2047 (mtpt) REVERT: D 591 LEU cc_start: 0.1339 (tp) cc_final: 0.0733 (pp) outliers start: 103 outliers final: 74 residues processed: 311 average time/residue: 0.1658 time to fit residues: 85.7174 Evaluate side-chains 290 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 205 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 193 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 90 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 263 optimal weight: 0.0670 chunk 176 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 305 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** 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 = 0.4207 r_free = 0.4207 target = 0.169302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127079 restraints weight = 52380.531| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.58 r_work: 0.3236 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29814 Z= 0.165 Angle : 0.690 12.321 40704 Z= 0.328 Chirality : 0.048 0.486 4777 Planarity : 0.004 0.048 5112 Dihedral : 6.869 58.985 5537 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 3.35 % Allowed : 22.34 % Favored : 74.32 % 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: -0.96 (0.14), residues: 3484 helix: 1.16 (0.17), residues: 990 sheet: -0.39 (0.19), residues: 743 loop : -1.88 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.021 0.001 TYR B1067 PHE 0.024 0.001 PHE B 140 TRP 0.021 0.001 TRP D 69 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00392 (29692) covalent geometry : angle 0.66428 (40378) SS BOND : bond 0.00512 ( 40) SS BOND : angle 1.76753 ( 80) hydrogen bonds : bond 0.03975 ( 1062) hydrogen bonds : angle 4.90712 ( 3018) link_BETA1-4 : bond 0.00612 ( 28) link_BETA1-4 : angle 2.13020 ( 84) link_NAG-ASN : bond 0.00311 ( 54) link_NAG-ASN : angle 2.36463 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 206 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6851 (mt0) cc_final: 0.6554 (mm-40) REVERT: A 200 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.5576 (m-80) REVERT: A 390 LEU cc_start: 0.6134 (mp) cc_final: 0.5661 (mt) REVERT: A 515 PHE cc_start: 0.7306 (m-80) cc_final: 0.6917 (m-80) REVERT: A 531 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 696 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8550 (p) REVERT: A 916 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9211 (tp) REVERT: B 111 ASP cc_start: 0.5747 (OUTLIER) cc_final: 0.4709 (p0) REVERT: B 137 ASN cc_start: 0.7347 (m-40) cc_final: 0.6518 (t0) REVERT: B 153 MET cc_start: 0.0514 (mpp) cc_final: -0.3672 (tmm) REVERT: B 558 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6574 (tmtt) REVERT: C 216 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5332 (tt) REVERT: C 347 PHE cc_start: 0.5406 (m-80) cc_final: 0.4931 (m-80) REVERT: C 417 LYS cc_start: 0.4008 (OUTLIER) cc_final: 0.2756 (tmmt) REVERT: C 1132 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9058 (pp) REVERT: D 79 LEU cc_start: 0.7595 (mt) cc_final: 0.7013 (tt) REVERT: D 115 ARG cc_start: 0.4822 (tpt170) cc_final: 0.4416 (tpp-160) REVERT: D 236 LEU cc_start: 0.4105 (mt) cc_final: 0.3709 (pp) REVERT: D 266 LEU cc_start: 0.1194 (OUTLIER) cc_final: 0.0673 (tp) REVERT: D 270 MET cc_start: 0.1711 (mmm) cc_final: 0.1197 (mtp) REVERT: D 309 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6778 (mttp) REVERT: D 344 CYS cc_start: 0.1853 (OUTLIER) cc_final: 0.1010 (t) REVERT: D 470 LYS cc_start: 0.2414 (mttm) cc_final: 0.1837 (mtpt) REVERT: D 591 LEU cc_start: 0.1272 (tp) cc_final: 0.0554 (pp) outliers start: 104 outliers final: 77 residues processed: 300 average time/residue: 0.1579 time to fit residues: 79.7919 Evaluate side-chains 284 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 115 optimal weight: 6.9990 chunk 300 optimal weight: 0.0570 chunk 157 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 320 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1071 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.166668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127396 restraints weight = 51792.283| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.54 r_work: 0.3202 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 29814 Z= 0.258 Angle : 0.812 20.888 40704 Z= 0.383 Chirality : 0.053 0.551 4777 Planarity : 0.005 0.053 5112 Dihedral : 7.753 58.888 5537 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.58 % Favored : 92.28 % Rotamer: Outliers : 3.48 % Allowed : 22.53 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3484 helix: 0.78 (0.17), residues: 996 sheet: -0.53 (0.19), residues: 744 loop : -2.00 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 102 TYR 0.028 0.002 TYR A 473 PHE 0.027 0.002 PHE D 555 TRP 0.018 0.002 TRP D 69 HIS 0.007 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00626 (29692) covalent geometry : angle 0.77221 (40378) SS BOND : bond 0.00504 ( 40) SS BOND : angle 2.05096 ( 80) hydrogen bonds : bond 0.04830 ( 1062) hydrogen bonds : angle 5.27816 ( 3018) link_BETA1-4 : bond 0.00645 ( 28) link_BETA1-4 : angle 2.58503 ( 84) link_NAG-ASN : bond 0.00695 ( 54) link_NAG-ASN : angle 3.41369 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 217 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6890 (mt0) cc_final: 0.6580 (mm-40) REVERT: A 200 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: A 226 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7512 (tt) REVERT: A 449 TYR cc_start: 0.6761 (m-80) cc_final: 0.6042 (m-80) REVERT: A 515 PHE cc_start: 0.7562 (m-80) cc_final: 0.7104 (m-80) REVERT: A 531 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7113 (p) REVERT: A 696 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 916 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9330 (tp) REVERT: B 111 ASP cc_start: 0.5459 (OUTLIER) cc_final: 0.4781 (p0) REVERT: B 137 ASN cc_start: 0.7368 (m-40) cc_final: 0.6576 (t0) REVERT: B 140 PHE cc_start: 0.7701 (p90) cc_final: 0.7300 (p90) REVERT: B 390 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6427 (tt) REVERT: B 558 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6621 (tmtt) REVERT: B 804 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8699 (mt0) REVERT: C 216 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5265 (tt) REVERT: C 347 PHE cc_start: 0.5453 (m-80) cc_final: 0.4933 (m-80) REVERT: C 1132 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9120 (pp) REVERT: D 79 LEU cc_start: 0.7827 (mt) cc_final: 0.7284 (tt) REVERT: D 115 ARG cc_start: 0.4717 (tpt170) cc_final: 0.4364 (tpp-160) REVERT: D 236 LEU cc_start: 0.4139 (mt) cc_final: 0.3653 (pp) REVERT: D 266 LEU cc_start: 0.1830 (OUTLIER) cc_final: 0.1575 (tp) REVERT: D 270 MET cc_start: 0.1949 (mmm) cc_final: 0.1399 (mtp) REVERT: D 309 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6778 (mttm) REVERT: D 332 MET cc_start: 0.3228 (ttp) cc_final: 0.2826 (ttp) REVERT: D 344 CYS cc_start: 0.2434 (OUTLIER) cc_final: 0.1596 (t) REVERT: D 470 LYS cc_start: 0.2306 (mttm) cc_final: 0.1639 (mtpt) REVERT: D 484 ILE cc_start: 0.2281 (mt) cc_final: 0.1895 (mm) REVERT: D 516 TYR cc_start: 0.4366 (t80) cc_final: 0.3770 (t80) REVERT: D 591 LEU cc_start: 0.1676 (tp) cc_final: 0.0414 (pp) outliers start: 108 outliers final: 84 residues processed: 312 average time/residue: 0.1552 time to fit residues: 81.6995 Evaluate side-chains 295 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 198 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 69 optimal weight: 0.0770 chunk 348 optimal weight: 0.7980 chunk 337 optimal weight: 20.0000 chunk 270 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 275 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.166876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127812 restraints weight = 51932.262| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.49 r_work: 0.3223 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 29814 Z= 0.278 Angle : 1.017 59.179 40704 Z= 0.515 Chirality : 0.055 1.177 4777 Planarity : 0.005 0.120 5112 Dihedral : 7.845 58.841 5537 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.72 % Favored : 92.11 % Rotamer: Outliers : 3.19 % Allowed : 22.66 % Favored : 74.16 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3484 helix: 0.78 (0.17), residues: 997 sheet: -0.55 (0.19), residues: 744 loop : -2.02 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 482 TYR 0.023 0.002 TYR B1067 PHE 0.023 0.002 PHE A 86 TRP 0.016 0.002 TRP D 69 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00612 (29692) covalent geometry : angle 0.96825 (40378) SS BOND : bond 0.01008 ( 40) SS BOND : angle 2.62683 ( 80) hydrogen bonds : bond 0.04630 ( 1062) hydrogen bonds : angle 5.27169 ( 3018) link_BETA1-4 : bond 0.00523 ( 28) link_BETA1-4 : angle 2.60374 ( 84) link_NAG-ASN : bond 0.00996 ( 54) link_NAG-ASN : angle 4.41238 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8609.69 seconds wall clock time: 147 minutes 34.99 seconds (8854.99 seconds total)