Starting phenix.real_space_refine on Fri Mar 6 09:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyz_26200/03_2026/7tyz_26200.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyz_26200/03_2026/7tyz_26200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tyz_26200/03_2026/7tyz_26200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyz_26200/03_2026/7tyz_26200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyz_26200/03_2026/7tyz_26200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyz_26200/03_2026/7tyz_26200.map" } resolution = 3.51 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= 0.017 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 129 5.16 5 C 18870 2.51 5 N 4899 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29736 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "C" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 7 Chain: "D" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "E" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 6 Chain: "F" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.46, per 1000 atoms: 0.25 Number of scatterers: 29736 At special positions: 0 Unit cell: (162.378, 159.759, 222.615, 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 129 16.00 O 5838 8.00 N 4899 7.00 C 18870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 603 " " NAG E1303 " - " ASN E 616 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 234 " " NAG E1306 " - " ASN E 165 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A 282 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN E 331 " " NAG T 1 " - " ASN E 709 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 282 " " NAG X 1 " - " ASN E 343 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 51 sheets defined 28.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.588A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.774A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.857A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.622A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.702A pdb=" N ALA A 623 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.265A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.821A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.659A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.517A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.547A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.180A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 27 through 37 removed outlier: 3.574A pdb=" N GLY B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.253A pdb=" N VAL B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.599A pdb=" N ASN B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.857A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.514A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.892A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.677A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.755A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.519A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.796A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.521A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.589A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.576A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.590A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.208A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 36 removed outlier: 3.533A pdb=" N ASN D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.094A pdb=" N VAL D 96 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.631A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 301 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.842A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.644A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.255A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN E 764 " --> pdb=" O CYS E 760 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 783 " --> pdb=" O GLN E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.797A pdb=" N GLN E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 883 " --> pdb=" O ALA E 879 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 907 Processing helix chain 'E' and resid 913 through 919 removed outlier: 3.608A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.542A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.675A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 983 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.247A pdb=" N GLU E 990 " --> pdb=" O PRO E 986 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1146 Processing helix chain 'F' and resid 16 through 25 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.579A pdb=" N GLU F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 123 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 158 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.025A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.853A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.625A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.801A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 145 removed outlier: 6.259A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 318 removed outlier: 5.464A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.827A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 659 removed outlier: 6.247A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.564A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.960A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 removed outlier: 6.463A pdb=" N ALA E 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.681A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.197A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.538A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.580A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.437A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.503A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.503A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 659 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.528A pdb=" N ALA C 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.963A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.943A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.917A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 263 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 50 through 55 removed outlier: 3.859A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 141 through 145 removed outlier: 6.502A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 310 through 318 removed outlier: 5.440A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 650 " --> pdb=" O PHE E 643 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 310 through 318 removed outlier: 5.440A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.996A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.996A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 510 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 452 through 453 removed outlier: 3.789A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 659 removed outlier: 6.222A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 712 through 715 Processing sheet with id=AF3, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.956A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 735 through 736 Processing sheet with id=AF5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 5.054A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1094 through 1097 1027 hydrogen bonds defined for protein. 2799 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: 7.23 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9527 1.34 - 1.47: 7444 1.47 - 1.59: 13243 1.59 - 1.71: 2 1.71 - 1.83: 165 Bond restraints: 30381 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.614 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C1 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 30376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 40292 1.81 - 3.61: 864 3.61 - 5.42: 139 5.42 - 7.22: 40 7.22 - 9.03: 5 Bond angle restraints: 41340 Sorted by residual: angle pdb=" CA LYS C 462 " pdb=" CB LYS C 462 " pdb=" CG LYS C 462 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C GLY C 404 " pdb=" N ASP C 405 " pdb=" CA ASP C 405 " ideal model delta sigma weight residual 120.38 125.06 -4.68 1.46e+00 4.69e-01 1.03e+01 angle pdb=" N GLN F 166 " pdb=" CA GLN F 166 " pdb=" CB GLN F 166 " ideal model delta sigma weight residual 110.39 115.23 -4.84 1.66e+00 3.63e-01 8.51e+00 angle pdb=" C SER E 359 " pdb=" N ASN E 360 " pdb=" CA ASN E 360 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" C CYS A 131 " pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sigma weight residual 114.41 108.05 6.36 2.30e+00 1.89e-01 7.66e+00 ... (remaining 41335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 17694 24.34 - 48.68: 970 48.68 - 73.02: 161 73.02 - 97.36: 76 97.36 - 121.71: 65 Dihedral angle restraints: 18966 sinusoidal: 8211 harmonic: 10755 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 11.73 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 14.56 78.44 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 15.19 77.81 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 18963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4857 0.159 - 0.319: 27 0.319 - 0.478: 6 0.478 - 0.637: 1 0.637 - 0.797: 2 Chirality restraints: 4893 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN E 282 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4890 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 282 " 0.036 2.00e-02 2.50e+03 3.26e-02 1.33e+01 pdb=" CG ASN E 282 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 282 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN E 282 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO C1143 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.027 2.00e-02 2.50e+03 2.62e-02 8.60e+00 pdb=" CG ASN A 616 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.020 2.00e-02 2.50e+03 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 715 2.68 - 3.24: 28527 3.24 - 3.79: 43990 3.79 - 4.35: 56725 4.35 - 4.90: 93907 Nonbonded interactions: 223864 Sorted by model distance: nonbonded pdb=" OG1 THR E 676 " pdb=" O SER E 691 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR C 676 " pdb=" O SER C 691 " model vdw 2.139 3.040 nonbonded pdb=" OD1 ASN A 616 " pdb=" N2 NAG A1303 " model vdw 2.169 3.120 nonbonded pdb=" OG SER A 803 " pdb=" OE1 GLN A 804 " model vdw 2.196 3.040 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.199 3.040 ... (remaining 223859 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 11.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 30.380 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.004 0.091 30489 Z= 0.183 Angle : 0.687 17.827 41622 Z= 0.316 Chirality : 0.052 0.797 4893 Planarity : 0.004 0.078 5277 Dihedral : 17.212 121.706 11922 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3663 helix: 1.14 (0.18), residues: 948 sheet: -0.60 (0.19), residues: 738 loop : -2.22 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 457 TYR 0.020 0.001 TYR A 421 PHE 0.016 0.001 PHE E 157 TRP 0.009 0.001 TRP F 79 HIS 0.005 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00384 (30381) covalent geometry : angle 0.63535 (41340) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.25243 ( 84) hydrogen bonds : bond 0.17701 ( 999) hydrogen bonds : angle 7.12215 ( 2799) link_ALPHA1-3 : bond 0.01396 ( 3) link_ALPHA1-3 : angle 2.60297 ( 9) link_BETA1-4 : bond 0.00924 ( 27) link_BETA1-4 : angle 3.08180 ( 81) link_NAG-ASN : bond 0.00889 ( 36) link_NAG-ASN : angle 4.29171 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 147 LYS cc_start: 0.5170 (mmtm) cc_final: 0.4925 (mttm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1814 time to fit residues: 58.2977 Evaluate side-chains 126 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 501 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN C 52 GLN C 148 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.119696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.074805 restraints weight = 83666.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077785 restraints weight = 45942.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076695 restraints weight = 26693.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076954 restraints weight = 28751.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077119 restraints weight = 26540.915| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 30489 Z= 0.302 Angle : 0.795 17.208 41622 Z= 0.383 Chirality : 0.051 0.376 4893 Planarity : 0.005 0.070 5277 Dihedral : 12.536 103.013 5322 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.84 % Allowed : 8.22 % Favored : 90.94 % 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: -1.79 (0.13), residues: 3663 helix: 0.59 (0.17), residues: 960 sheet: -0.91 (0.18), residues: 756 loop : -2.31 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 457 TYR 0.028 0.002 TYR A 421 PHE 0.032 0.002 PHE C 906 TRP 0.017 0.002 TRP E 152 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00708 (30381) covalent geometry : angle 0.75462 (41340) SS BOND : bond 0.00592 ( 42) SS BOND : angle 1.91233 ( 84) hydrogen bonds : bond 0.05757 ( 999) hydrogen bonds : angle 5.64777 ( 2799) link_ALPHA1-3 : bond 0.02434 ( 3) link_ALPHA1-3 : angle 2.07359 ( 9) link_BETA1-4 : bond 0.01198 ( 27) link_BETA1-4 : angle 3.52599 ( 81) link_NAG-ASN : bond 0.00642 ( 36) link_NAG-ASN : angle 3.61928 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 HIS cc_start: 0.6377 (t70) cc_final: 0.6169 (t70) REVERT: D 79 TRP cc_start: 0.2283 (t60) cc_final: 0.1648 (m100) REVERT: D 147 LYS cc_start: 0.4488 (mmtm) cc_final: 0.4082 (mttm) REVERT: E 583 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7341 (tm-30) outliers start: 27 outliers final: 18 residues processed: 162 average time/residue: 0.1612 time to fit residues: 44.8411 Evaluate side-chains 141 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 338 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 186 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 188 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 804 GLN C 935 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.123130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078072 restraints weight = 82886.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081180 restraints weight = 42067.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081391 restraints weight = 23959.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.081790 restraints weight = 22596.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082022 restraints weight = 19526.744| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30489 Z= 0.117 Angle : 0.640 17.951 41622 Z= 0.302 Chirality : 0.046 0.340 4893 Planarity : 0.004 0.067 5277 Dihedral : 10.813 105.119 5322 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.06 % Allowed : 10.62 % Favored : 88.32 % 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: -1.49 (0.14), residues: 3663 helix: 0.89 (0.17), residues: 972 sheet: -0.71 (0.18), residues: 756 loop : -2.19 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 81 TYR 0.020 0.001 TYR A 473 PHE 0.014 0.001 PHE E 377 TRP 0.016 0.001 TRP E 258 HIS 0.008 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00249 (30381) covalent geometry : angle 0.60181 (41340) SS BOND : bond 0.00268 ( 42) SS BOND : angle 1.06517 ( 84) hydrogen bonds : bond 0.04218 ( 999) hydrogen bonds : angle 5.10844 ( 2799) link_ALPHA1-3 : bond 0.02418 ( 3) link_ALPHA1-3 : angle 2.41451 ( 9) link_BETA1-4 : bond 0.01082 ( 27) link_BETA1-4 : angle 3.26808 ( 81) link_NAG-ASN : bond 0.00626 ( 36) link_NAG-ASN : angle 3.13323 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8610 (t80) REVERT: C 157 PHE cc_start: 0.6443 (t80) cc_final: 0.5611 (m-10) REVERT: C 160 TYR cc_start: 0.7115 (p90) cc_final: 0.6709 (p90) REVERT: D 52 HIS cc_start: 0.6197 (t70) cc_final: 0.5945 (t70) REVERT: D 147 LYS cc_start: 0.4443 (mmtm) cc_final: 0.4042 (mttm) REVERT: E 115 GLN cc_start: 0.7559 (tp-100) cc_final: 0.7341 (tp40) REVERT: E 583 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7309 (tm-30) outliers start: 34 outliers final: 18 residues processed: 178 average time/residue: 0.1676 time to fit residues: 50.5651 Evaluate side-chains 147 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 22 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 303 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 243 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 41 ASN F 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.123213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078248 restraints weight = 82630.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081262 restraints weight = 42292.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081586 restraints weight = 24525.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082091 restraints weight = 23113.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082141 restraints weight = 19695.529| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30489 Z= 0.112 Angle : 0.622 18.119 41622 Z= 0.291 Chirality : 0.045 0.360 4893 Planarity : 0.004 0.068 5277 Dihedral : 9.553 102.670 5322 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.28 % Allowed : 12.03 % Favored : 86.69 % 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: -1.36 (0.14), residues: 3663 helix: 1.03 (0.17), residues: 972 sheet: -0.54 (0.18), residues: 774 loop : -2.18 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1107 TYR 0.017 0.001 TYR A 421 PHE 0.012 0.001 PHE E 377 TRP 0.008 0.001 TRP E 353 HIS 0.010 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00246 (30381) covalent geometry : angle 0.58555 (41340) SS BOND : bond 0.00223 ( 42) SS BOND : angle 1.01288 ( 84) hydrogen bonds : bond 0.03807 ( 999) hydrogen bonds : angle 4.82786 ( 2799) link_ALPHA1-3 : bond 0.02220 ( 3) link_ALPHA1-3 : angle 2.32985 ( 9) link_BETA1-4 : bond 0.01000 ( 27) link_BETA1-4 : angle 3.22740 ( 81) link_NAG-ASN : bond 0.00496 ( 36) link_NAG-ASN : angle 2.98094 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8573 (t80) REVERT: C 157 PHE cc_start: 0.6458 (t80) cc_final: 0.5605 (m-10) REVERT: C 160 TYR cc_start: 0.7164 (p90) cc_final: 0.6740 (p90) REVERT: D 147 LYS cc_start: 0.4419 (mmtm) cc_final: 0.4011 (mttm) outliers start: 41 outliers final: 24 residues processed: 168 average time/residue: 0.1540 time to fit residues: 44.7545 Evaluate side-chains 150 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 356 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 347 optimal weight: 0.4980 chunk 176 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 52 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 = 0.4062 r_free = 0.4062 target = 0.122238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.076865 restraints weight = 83400.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079725 restraints weight = 42609.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079683 restraints weight = 29612.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080351 restraints weight = 22068.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080457 restraints weight = 19403.890| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30489 Z= 0.138 Angle : 0.627 18.030 41622 Z= 0.295 Chirality : 0.045 0.342 4893 Planarity : 0.004 0.064 5277 Dihedral : 8.817 99.807 5322 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.53 % Allowed : 12.90 % Favored : 85.57 % 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: -1.34 (0.14), residues: 3663 helix: 1.05 (0.17), residues: 972 sheet: -0.62 (0.18), residues: 786 loop : -2.13 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 457 TYR 0.020 0.001 TYR A 473 PHE 0.011 0.001 PHE C 565 TRP 0.008 0.001 TRP E 258 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00317 (30381) covalent geometry : angle 0.59116 (41340) SS BOND : bond 0.00271 ( 42) SS BOND : angle 1.21688 ( 84) hydrogen bonds : bond 0.04029 ( 999) hydrogen bonds : angle 4.78248 ( 2799) link_ALPHA1-3 : bond 0.02225 ( 3) link_ALPHA1-3 : angle 2.37762 ( 9) link_BETA1-4 : bond 0.00993 ( 27) link_BETA1-4 : angle 3.08856 ( 81) link_NAG-ASN : bond 0.00482 ( 36) link_NAG-ASN : angle 3.02143 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8588 (t80) REVERT: C 157 PHE cc_start: 0.6513 (t80) cc_final: 0.5652 (m-10) REVERT: C 160 TYR cc_start: 0.7251 (p90) cc_final: 0.6774 (p90) REVERT: C 329 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7709 (t80) REVERT: D 147 LYS cc_start: 0.4429 (mmtm) cc_final: 0.4053 (mttm) REVERT: E 329 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8721 (t80) REVERT: E 583 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7242 (tm-30) outliers start: 49 outliers final: 34 residues processed: 168 average time/residue: 0.1636 time to fit residues: 47.5032 Evaluate side-chains 164 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 260 optimal weight: 0.4980 chunk 354 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071444 restraints weight = 83195.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073566 restraints weight = 40172.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074907 restraints weight = 26355.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075681 restraints weight = 20717.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076154 restraints weight = 18092.665| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 30489 Z= 0.337 Angle : 0.789 17.641 41622 Z= 0.381 Chirality : 0.049 0.340 4893 Planarity : 0.005 0.067 5277 Dihedral : 8.816 95.112 5322 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 1.87 % Allowed : 13.62 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.13), residues: 3663 helix: 0.58 (0.17), residues: 957 sheet: -0.79 (0.19), residues: 735 loop : -2.44 (0.12), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 408 TYR 0.023 0.002 TYR A 421 PHE 0.023 0.002 PHE C 565 TRP 0.018 0.002 TRP A 152 HIS 0.005 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00792 (30381) covalent geometry : angle 0.75484 (41340) SS BOND : bond 0.00778 ( 42) SS BOND : angle 1.99754 ( 84) hydrogen bonds : bond 0.05751 ( 999) hydrogen bonds : angle 5.34207 ( 2799) link_ALPHA1-3 : bond 0.02313 ( 3) link_ALPHA1-3 : angle 2.40980 ( 9) link_BETA1-4 : bond 0.01020 ( 27) link_BETA1-4 : angle 3.12156 ( 81) link_NAG-ASN : bond 0.00687 ( 36) link_NAG-ASN : angle 3.31084 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: C 157 PHE cc_start: 0.6430 (t80) cc_final: 0.6148 (m-10) REVERT: C 583 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7372 (tm-30) REVERT: D 147 LYS cc_start: 0.4105 (mmtm) cc_final: 0.3836 (mttm) REVERT: E 137 ASN cc_start: 0.6853 (t0) cc_final: 0.6375 (m-40) outliers start: 60 outliers final: 45 residues processed: 182 average time/residue: 0.1589 time to fit residues: 50.5380 Evaluate side-chains 166 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 896 ILE Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 188 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 346 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN F 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.121236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076430 restraints weight = 82747.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.079591 restraints weight = 42055.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079551 restraints weight = 24023.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080044 restraints weight = 22608.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080182 restraints weight = 19903.216| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30489 Z= 0.123 Angle : 0.638 18.203 41622 Z= 0.303 Chirality : 0.045 0.361 4893 Planarity : 0.004 0.079 5277 Dihedral : 8.077 92.652 5322 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.89 % Favored : 92.08 % Rotamer: Outliers : 1.34 % Allowed : 14.68 % Favored : 83.97 % 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: -1.47 (0.14), residues: 3663 helix: 1.02 (0.17), residues: 954 sheet: -0.67 (0.19), residues: 756 loop : -2.23 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 457 TYR 0.022 0.001 TYR A 473 PHE 0.025 0.001 PHE C 168 TRP 0.008 0.001 TRP F 79 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00271 (30381) covalent geometry : angle 0.60200 (41340) SS BOND : bond 0.00289 ( 42) SS BOND : angle 1.33598 ( 84) hydrogen bonds : bond 0.04205 ( 999) hydrogen bonds : angle 4.86265 ( 2799) link_ALPHA1-3 : bond 0.02145 ( 3) link_ALPHA1-3 : angle 2.59669 ( 9) link_BETA1-4 : bond 0.01093 ( 27) link_BETA1-4 : angle 3.06448 ( 81) link_NAG-ASN : bond 0.00443 ( 36) link_NAG-ASN : angle 3.03184 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8583 (t80) REVERT: C 84 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (mm) REVERT: C 157 PHE cc_start: 0.6585 (t80) cc_final: 0.6121 (m-10) REVERT: C 160 TYR cc_start: 0.7385 (p90) cc_final: 0.7111 (p90) REVERT: C 329 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7778 (t80) REVERT: D 147 LYS cc_start: 0.4515 (mmtm) cc_final: 0.4123 (mttm) REVERT: E 137 ASN cc_start: 0.6733 (t0) cc_final: 0.6193 (m-40) REVERT: E 329 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8625 (t80) outliers start: 43 outliers final: 27 residues processed: 167 average time/residue: 0.1584 time to fit residues: 45.9599 Evaluate side-chains 156 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 76 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 242 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.122128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075375 restraints weight = 86546.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077519 restraints weight = 40760.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078890 restraints weight = 26430.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079729 restraints weight = 20561.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080139 restraints weight = 17786.685| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30489 Z= 0.221 Angle : 0.692 17.588 41622 Z= 0.331 Chirality : 0.046 0.350 4893 Planarity : 0.005 0.076 5277 Dihedral : 7.908 90.807 5322 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.40 % Favored : 89.57 % Rotamer: Outliers : 1.44 % Allowed : 15.09 % Favored : 83.47 % 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: -1.61 (0.13), residues: 3663 helix: 0.90 (0.17), residues: 957 sheet: -0.79 (0.18), residues: 762 loop : -2.30 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1107 TYR 0.021 0.001 TYR C 473 PHE 0.018 0.002 PHE C 168 TRP 0.013 0.001 TRP C 152 HIS 0.005 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00526 (30381) covalent geometry : angle 0.65845 (41340) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.55304 ( 84) hydrogen bonds : bond 0.04797 ( 999) hydrogen bonds : angle 4.97072 ( 2799) link_ALPHA1-3 : bond 0.02045 ( 3) link_ALPHA1-3 : angle 2.46119 ( 9) link_BETA1-4 : bond 0.01031 ( 27) link_BETA1-4 : angle 3.05117 ( 81) link_NAG-ASN : bond 0.00498 ( 36) link_NAG-ASN : angle 2.99501 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 PHE cc_start: 0.6263 (t80) cc_final: 0.5984 (m-10) REVERT: D 147 LYS cc_start: 0.4142 (mmtm) cc_final: 0.3868 (mttm) REVERT: E 137 ASN cc_start: 0.6843 (t0) cc_final: 0.6417 (m-40) outliers start: 46 outliers final: 39 residues processed: 158 average time/residue: 0.1596 time to fit residues: 43.8738 Evaluate side-chains 158 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1027 THR Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 329 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 200 optimal weight: 0.0170 chunk 261 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.121097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076177 restraints weight = 83134.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079637 restraints weight = 41767.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079392 restraints weight = 24930.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079723 restraints weight = 21231.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079897 restraints weight = 20087.934| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30489 Z= 0.127 Angle : 0.636 17.767 41622 Z= 0.303 Chirality : 0.045 0.355 4893 Planarity : 0.004 0.073 5277 Dihedral : 7.498 88.702 5322 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.03 % Favored : 91.95 % Rotamer: Outliers : 1.41 % Allowed : 15.25 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3663 helix: 1.08 (0.17), residues: 957 sheet: -0.66 (0.19), residues: 747 loop : -2.22 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 457 TYR 0.021 0.001 TYR C 473 PHE 0.021 0.001 PHE C 168 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00288 (30381) covalent geometry : angle 0.60316 (41340) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.31799 ( 84) hydrogen bonds : bond 0.04132 ( 999) hydrogen bonds : angle 4.75739 ( 2799) link_ALPHA1-3 : bond 0.02289 ( 3) link_ALPHA1-3 : angle 2.67538 ( 9) link_BETA1-4 : bond 0.00990 ( 27) link_BETA1-4 : angle 3.01519 ( 81) link_NAG-ASN : bond 0.00424 ( 36) link_NAG-ASN : angle 2.83419 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8600 (t80) REVERT: C 84 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8095 (mm) REVERT: C 157 PHE cc_start: 0.6465 (t80) cc_final: 0.6085 (m-10) REVERT: C 160 TYR cc_start: 0.7432 (p90) cc_final: 0.7169 (p90) REVERT: D 147 LYS cc_start: 0.4485 (mmtm) cc_final: 0.4108 (mttm) REVERT: E 137 ASN cc_start: 0.6834 (t0) cc_final: 0.6270 (m-40) REVERT: E 329 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8687 (t80) outliers start: 45 outliers final: 36 residues processed: 170 average time/residue: 0.1566 time to fit residues: 46.1464 Evaluate side-chains 160 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 118 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 310 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.120255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075237 restraints weight = 82624.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078640 restraints weight = 41829.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078415 restraints weight = 25147.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078830 restraints weight = 21307.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078913 restraints weight = 19464.721| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30489 Z= 0.168 Angle : 0.659 17.632 41622 Z= 0.314 Chirality : 0.045 0.355 4893 Planarity : 0.004 0.072 5277 Dihedral : 7.371 87.211 5322 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.72 % Favored : 90.25 % Rotamer: Outliers : 1.34 % Allowed : 15.43 % Favored : 83.22 % 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: -1.48 (0.14), residues: 3663 helix: 1.03 (0.17), residues: 957 sheet: -0.68 (0.19), residues: 741 loop : -2.24 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.021 0.001 TYR C 473 PHE 0.018 0.001 PHE C 168 TRP 0.039 0.001 TRP E 353 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00393 (30381) covalent geometry : angle 0.62654 (41340) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.43846 ( 84) hydrogen bonds : bond 0.04371 ( 999) hydrogen bonds : angle 4.79317 ( 2799) link_ALPHA1-3 : bond 0.02045 ( 3) link_ALPHA1-3 : angle 2.58288 ( 9) link_BETA1-4 : bond 0.01007 ( 27) link_BETA1-4 : angle 2.99349 ( 81) link_NAG-ASN : bond 0.00438 ( 36) link_NAG-ASN : angle 2.84583 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (mm) REVERT: C 157 PHE cc_start: 0.6519 (t80) cc_final: 0.6137 (m-10) REVERT: C 160 TYR cc_start: 0.7459 (p90) cc_final: 0.7209 (p90) REVERT: D 147 LYS cc_start: 0.4455 (mmtm) cc_final: 0.4042 (mttm) REVERT: E 137 ASN cc_start: 0.6856 (t0) cc_final: 0.6396 (m-40) REVERT: E 383 SER cc_start: 0.7812 (m) cc_final: 0.7584 (t) REVERT: E 633 TRP cc_start: 0.6092 (OUTLIER) cc_final: 0.5667 (p90) outliers start: 43 outliers final: 40 residues processed: 160 average time/residue: 0.1607 time to fit residues: 44.6704 Evaluate side-chains 163 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 633 TRP Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1027 THR Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 303 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 298 optimal weight: 8.9990 chunk 301 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.118166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073423 restraints weight = 83413.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076546 restraints weight = 41756.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.076479 restraints weight = 28205.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076841 restraints weight = 21316.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077093 restraints weight = 19721.900| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 30489 Z= 0.279 Angle : 0.750 17.605 41622 Z= 0.364 Chirality : 0.048 0.358 4893 Planarity : 0.005 0.072 5277 Dihedral : 7.728 86.253 5322 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.00 % Favored : 88.94 % Rotamer: Outliers : 1.44 % Allowed : 15.56 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 3663 helix: 0.71 (0.17), residues: 954 sheet: -0.86 (0.19), residues: 720 loop : -2.41 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 408 TYR 0.022 0.002 TYR C 473 PHE 0.019 0.002 PHE C 565 TRP 0.025 0.002 TRP E 353 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00660 (30381) covalent geometry : angle 0.71843 (41340) SS BOND : bond 0.00516 ( 42) SS BOND : angle 1.86173 ( 84) hydrogen bonds : bond 0.05407 ( 999) hydrogen bonds : angle 5.13765 ( 2799) link_ALPHA1-3 : bond 0.01987 ( 3) link_ALPHA1-3 : angle 2.61915 ( 9) link_BETA1-4 : bond 0.01014 ( 27) link_BETA1-4 : angle 2.96450 ( 81) link_NAG-ASN : bond 0.00572 ( 36) link_NAG-ASN : angle 3.09207 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.32 seconds wall clock time: 94 minutes 40.32 seconds (5680.32 seconds total)