Starting phenix.real_space_refine on Sun Jul 5 19:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyz_26200/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyz_26200/07_2026/7tyz_26200.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 5.53, per 1000 atoms: 0.19 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: 2.08 Conformation dependent library (CDL) restraints added in 1.3 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: 1.18 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: 5.21 Time building geometry restraints manager: 2.78 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 - 17.96: 15877 17.96 - 35.92: 1411 35.92 - 53.88: 220 53.88 - 71.84: 63 71.84 - 89.80: 33 Dihedral angle restraints: 17604 sinusoidal: 6849 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 17601 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: 9.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.630 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 14.065 89.800 10560 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/Z covalent geometry : bond 0.00384 / 0.18 (30381) covalent geometry : angle 0.63535 / 0.30 (41340) SS BOND : bond 0.00258 / 0.17 ( 42) SS BOND : angle 1.25243 / 0.75 ( 84) hydrogen bonds : bond 0.17701 / 11.57 ( 999) hydrogen bonds : angle 7.12215 / 4.94 ( 2799) link_ALPHA1-3 : bond 0.01396 / 0.67 ( 3) link_ALPHA1-3 : angle 2.60297 / 1.53 ( 9) link_BETA1-4 : bond 0.00924 / 0.66 ( 27) link_BETA1-4 : angle 3.08180 / 2.26 ( 81) link_NAG-ASN : bond 0.00889 / 0.54 ( 36) link_NAG-ASN : angle 4.29171 / 2.89 ( 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 : 1.046 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: 0.1738 time to fit residues: 55.5494 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 : 1.114 ------------------------------------------------------------------------------- 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... 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 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 = 0.119785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075446 restraints weight = 83877.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077392 restraints weight = 47865.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076898 restraints weight = 30140.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077350 restraints weight = 31046.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077334 restraints weight = 26225.213| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 30489 Z= 0.304 Angle : 0.775 17.440 41622 Z= 0.379 Chirality : 0.050 0.355 4893 Planarity : 0.005 0.070 5277 Dihedral : 4.840 29.351 3960 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.81 % Allowed : 8.50 % Favored : 90.69 % 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: -1.77 (0.13), residues: 3663 helix: 0.71 (0.17), residues: 933 sheet: -0.91 (0.18), residues: 756 loop : -2.31 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 457 TYR 0.028 0.002 TYR A 421 PHE 0.033 0.002 PHE C 906 TRP 0.019 0.002 TRP E 152 HIS 0.008 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.30 (30381) covalent geometry : angle 0.74090 / 0.37 (41340) SS BOND : bond 0.00563 / 0.34 ( 42) SS BOND : angle 1.90396 / 1.14 ( 84) hydrogen bonds : bond 0.05741 / 3.72 ( 999) hydrogen bonds : angle 5.63239 / 3.90 ( 2799) link_ALPHA1-3 : bond 0.01451 / 0.70 ( 3) link_ALPHA1-3 : angle 2.03136 / 1.14 ( 9) link_BETA1-4 : bond 0.01135 / 0.83 ( 27) link_BETA1-4 : angle 2.84938 / 2.12 ( 81) link_NAG-ASN : bond 0.00614 / 0.37 ( 36) link_NAG-ASN : angle 3.49997 / 2.41 ( 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 168 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 HIS cc_start: 0.6389 (t70) cc_final: 0.6178 (t70) REVERT: D 79 TRP cc_start: 0.2274 (t60) cc_final: 0.1608 (m100) REVERT: D 147 LYS cc_start: 0.4430 (mmtm) cc_final: 0.4027 (mttm) REVERT: E 583 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7429 (tm-30) outliers start: 26 outliers final: 17 residues processed: 161 average time/residue: 0.1763 time to fit residues: 48.5833 Evaluate side-chains 139 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 191 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 chunk 186 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.122125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.076726 restraints weight = 82901.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079635 restraints weight = 42123.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079563 restraints weight = 28889.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080150 restraints weight = 22039.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080392 restraints weight = 19884.830| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1443 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= 0.131 Angle : 0.625 17.858 41622 Z= 0.301 Chirality : 0.045 0.485 4893 Planarity : 0.004 0.068 5277 Dihedral : 4.542 26.831 3960 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.00 % Allowed : 10.78 % Favored : 88.22 % 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: -1.60 (0.13), residues: 3663 helix: 0.85 (0.17), residues: 957 sheet: -0.71 (0.18), residues: 750 loop : -2.29 (0.13), residues: 1956 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 0.013 0.001 PHE A 823 TRP 0.012 0.001 TRP E 258 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (30381) covalent geometry : angle 0.59130 / 0.29 (41340) SS BOND : bond 0.00304 / 0.19 ( 42) SS BOND : angle 1.21569 / 0.74 ( 84) hydrogen bonds : bond 0.04513 / 2.92 ( 999) hydrogen bonds : angle 5.18535 / 3.59 ( 2799) link_ALPHA1-3 : bond 0.01300 / 0.63 ( 3) link_ALPHA1-3 : angle 2.07917 / 1.12 ( 9) link_BETA1-4 : bond 0.01058 / 0.78 ( 27) link_BETA1-4 : angle 2.69352 / 1.99 ( 81) link_NAG-ASN : bond 0.00559 / 0.35 ( 36) link_NAG-ASN : angle 3.10000 / 2.18 ( 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 172 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8583 (t80) REVERT: C 157 PHE cc_start: 0.6551 (t80) cc_final: 0.5729 (m-10) REVERT: C 160 TYR cc_start: 0.7099 (p90) cc_final: 0.6635 (p90) REVERT: D 52 HIS cc_start: 0.6140 (t70) cc_final: 0.5911 (t70) REVERT: D 147 LYS cc_start: 0.4371 (mmtm) cc_final: 0.3969 (mttm) REVERT: E 583 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7313 (tm-30) outliers start: 32 outliers final: 19 residues processed: 168 average time/residue: 0.1658 time to fit residues: 47.4828 Evaluate side-chains 144 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 895 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: 10.0000 chunk 303 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.119425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073947 restraints weight = 82688.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076901 restraints weight = 42095.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.076741 restraints weight = 28799.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.077293 restraints weight = 22109.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077472 restraints weight = 20158.149| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 30489 Z= 0.238 Angle : 0.696 18.142 41622 Z= 0.338 Chirality : 0.047 0.368 4893 Planarity : 0.005 0.068 5277 Dihedral : 4.773 30.436 3960 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 1.72 % Allowed : 12.15 % Favored : 86.13 % 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: -1.79 (0.13), residues: 3663 helix: 0.67 (0.17), residues: 951 sheet: -0.76 (0.19), residues: 729 loop : -2.41 (0.12), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 905 TYR 0.023 0.002 TYR A 421 PHE 0.017 0.002 PHE C 906 TRP 0.012 0.002 TRP A 152 HIS 0.011 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (30381) covalent geometry : angle 0.66678 / 0.33 (41340) SS BOND : bond 0.00469 / 0.28 ( 42) SS BOND : angle 1.57308 / 0.95 ( 84) hydrogen bonds : bond 0.05239 / 3.39 ( 999) hydrogen bonds : angle 5.24514 / 3.63 ( 2799) link_ALPHA1-3 : bond 0.00991 / 0.48 ( 3) link_ALPHA1-3 : angle 2.12735 / 1.19 ( 9) link_BETA1-4 : bond 0.01064 / 0.79 ( 27) link_BETA1-4 : angle 2.68500 / 1.99 ( 81) link_NAG-ASN : bond 0.00560 / 0.36 ( 36) link_NAG-ASN : angle 2.96263 / 2.05 ( 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 189 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.177 Fit side-chains REVERT: A 329 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8566 (t80) REVERT: A 425 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7502 (tp) REVERT: A 731 MET cc_start: 0.8992 (ptt) cc_final: 0.8587 (ptt) REVERT: C 157 PHE cc_start: 0.6660 (t80) cc_final: 0.6099 (m-10) REVERT: D 147 LYS cc_start: 0.4355 (mmtm) cc_final: 0.3950 (mttm) REVERT: E 781 VAL cc_start: 0.9615 (OUTLIER) cc_final: 0.9407 (p) REVERT: E 1029 MET cc_start: 0.9045 (tpp) cc_final: 0.8673 (ttm) outliers start: 55 outliers final: 38 residues processed: 179 average time/residue: 0.1769 time to fit residues: 54.1832 Evaluate side-chains 162 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 425 LEU 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 597 VAL 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 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 318 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 C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU 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 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 781 VAL Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1027 THR 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: 30.0000 chunk 261 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 347 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.117447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072438 restraints weight = 84094.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075116 restraints weight = 43429.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075047 restraints weight = 27075.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075427 restraints weight = 29407.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075607 restraints weight = 23432.091| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 30489 Z= 0.324 Angle : 0.774 18.222 41622 Z= 0.381 Chirality : 0.050 0.337 4893 Planarity : 0.005 0.076 5277 Dihedral : 5.172 30.454 3960 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 2.53 % Allowed : 13.68 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 3663 helix: 0.37 (0.17), residues: 957 sheet: -0.98 (0.19), residues: 729 loop : -2.59 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 408 TYR 0.025 0.002 TYR A 421 PHE 0.019 0.002 PHE A 906 TRP 0.017 0.002 TRP A 152 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.32 (30381) covalent geometry : angle 0.74672 / 0.37 (41340) SS BOND : bond 0.00730 / 0.41 ( 42) SS BOND : angle 1.83669 / 1.08 ( 84) hydrogen bonds : bond 0.05728 / 3.73 ( 999) hydrogen bonds : angle 5.48824 / 3.81 ( 2799) link_ALPHA1-3 : bond 0.00679 / 0.33 ( 3) link_ALPHA1-3 : angle 2.09767 / 1.25 ( 9) link_BETA1-4 : bond 0.01007 / 0.74 ( 27) link_BETA1-4 : angle 2.75238 / 2.04 ( 81) link_NAG-ASN : bond 0.00584 / 0.36 ( 36) link_NAG-ASN : angle 2.99979 / 2.07 ( 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 214 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 133 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7770 (tt) cc_final: 0.7474 (tt) REVERT: A 731 MET cc_start: 0.9194 (ptt) cc_final: 0.8956 (ptt) REVERT: C 157 PHE cc_start: 0.6694 (t80) cc_final: 0.6136 (m-80) REVERT: C 210 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7682 (tp) REVERT: D 147 LYS cc_start: 0.4480 (mmtm) cc_final: 0.4093 (mttm) REVERT: E 137 ASN cc_start: 0.6885 (t0) cc_final: 0.6445 (m-40) REVERT: E 633 TRP cc_start: 0.6267 (OUTLIER) cc_final: 0.5839 (p90) outliers start: 81 outliers final: 53 residues processed: 205 average time/residue: 0.1612 time to fit residues: 58.0312 Evaluate side-chains 177 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL 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 781 VAL Chi-restraints excluded: chain A residue 881 THR 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 210 ILE 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 400 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 882 ILE 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 1027 THR 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 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 597 VAL Chi-restraints excluded: chain E residue 599 THR 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 882 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 896 ILE Chi-restraints excluded: chain E residue 931 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 260 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 233 optimal weight: 30.0000 chunk 168 optimal weight: 0.5980 chunk 242 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 234 optimal weight: 0.3980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 41 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.119489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073527 restraints weight = 82776.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075677 restraints weight = 39204.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077041 restraints weight = 25530.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.077801 restraints weight = 19926.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078325 restraints weight = 17356.857| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30489 Z= 0.161 Angle : 0.650 17.819 41622 Z= 0.316 Chirality : 0.046 0.345 4893 Planarity : 0.005 0.068 5277 Dihedral : 4.871 30.022 3960 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.00 % Allowed : 15.37 % Favored : 82.63 % 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: -1.79 (0.13), residues: 3663 helix: 0.69 (0.17), residues: 957 sheet: -0.78 (0.19), residues: 726 loop : -2.42 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 457 TYR 0.024 0.001 TYR C 473 PHE 0.024 0.001 PHE C 168 TRP 0.009 0.001 TRP C 152 HIS 0.005 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (30381) covalent geometry : angle 0.62150 / 0.31 (41340) SS BOND : bond 0.00336 / 0.21 ( 42) SS BOND : angle 1.51840 / 0.88 ( 84) hydrogen bonds : bond 0.04641 / 3.01 ( 999) hydrogen bonds : angle 5.07826 / 3.52 ( 2799) link_ALPHA1-3 : bond 0.00748 / 0.37 ( 3) link_ALPHA1-3 : angle 1.83232 / 1.08 ( 9) link_BETA1-4 : bond 0.00984 / 0.72 ( 27) link_BETA1-4 : angle 2.64011 / 1.95 ( 81) link_NAG-ASN : bond 0.00429 / 0.27 ( 36) link_NAG-ASN : angle 2.74726 / 1.91 ( 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 196 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 132 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8689 (t80) REVERT: A 731 MET cc_start: 0.9013 (ptt) cc_final: 0.8725 (ptt) REVERT: C 425 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7317 (tp) REVERT: C 554 GLU cc_start: 0.7640 (mp0) cc_final: 0.7416 (mp0) REVERT: D 147 LYS cc_start: 0.4100 (mmtm) cc_final: 0.3850 (mttm) REVERT: E 137 ASN cc_start: 0.6898 (t0) cc_final: 0.6467 (m-40) REVERT: E 633 TRP cc_start: 0.6136 (OUTLIER) cc_final: 0.5735 (p90) outliers start: 64 outliers final: 44 residues processed: 188 average time/residue: 0.1511 time to fit residues: 49.7511 Evaluate side-chains 169 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 453 TYR Chi-restraints excluded: chain A residue 500 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 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 125 ASN 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 425 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1027 THR 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 329 PHE Chi-restraints excluded: chain E residue 439 ASN Chi-restraints excluded: chain E residue 452 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 599 THR Chi-restraints excluded: chain E residue 633 TRP 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 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: 5.9990 chunk 223 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 346 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 301 optimal weight: 0.0770 chunk 7 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.122509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076834 restraints weight = 85986.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079000 restraints weight = 39392.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080361 restraints weight = 25147.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081163 restraints weight = 19401.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081665 restraints weight = 16731.384| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30489 Z= 0.158 Angle : 0.649 17.947 41622 Z= 0.315 Chirality : 0.045 0.349 4893 Planarity : 0.004 0.067 5277 Dihedral : 4.806 28.423 3960 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.66 % Favored : 90.31 % Rotamer: Outliers : 2.03 % Allowed : 15.78 % Favored : 82.19 % 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: -1.67 (0.13), residues: 3663 helix: 0.82 (0.17), residues: 957 sheet: -0.77 (0.19), residues: 747 loop : -2.35 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 457 TYR 0.023 0.001 TYR C 473 PHE 0.019 0.001 PHE C 168 TRP 0.009 0.001 TRP A 152 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (30381) covalent geometry : angle 0.62008 / 0.31 (41340) SS BOND : bond 0.00424 / 0.25 ( 42) SS BOND : angle 1.69403 / 0.99 ( 84) hydrogen bonds : bond 0.04500 / 2.92 ( 999) hydrogen bonds : angle 5.01895 / 3.48 ( 2799) link_ALPHA1-3 : bond 0.00734 / 0.37 ( 3) link_ALPHA1-3 : angle 1.72315 / 1.03 ( 9) link_BETA1-4 : bond 0.01042 / 0.77 ( 27) link_BETA1-4 : angle 2.63174 / 1.96 ( 81) link_NAG-ASN : bond 0.00399 / 0.25 ( 36) link_NAG-ASN : angle 2.69778 / 1.87 ( 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 191 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 731 MET cc_start: 0.9051 (ptt) cc_final: 0.8767 (ptt) REVERT: C 84 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8246 (mm) REVERT: C 425 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7452 (tp) REVERT: D 147 LYS cc_start: 0.3906 (mmtm) cc_final: 0.3658 (mttm) REVERT: E 137 ASN cc_start: 0.6877 (t0) cc_final: 0.6515 (m-40) REVERT: E 329 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8689 (t80) REVERT: E 633 TRP cc_start: 0.6152 (OUTLIER) cc_final: 0.5747 (p90) outliers start: 65 outliers final: 49 residues processed: 185 average time/residue: 0.1580 time to fit residues: 51.3401 Evaluate side-chains 173 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS 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 B residue 18 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 125 ASN 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 425 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1027 THR 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 329 PHE Chi-restraints excluded: chain E residue 452 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 599 THR Chi-restraints excluded: chain E residue 633 TRP 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 1027 THR 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: 2.9990 chunk 363 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.119056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.074823 restraints weight = 83418.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078182 restraints weight = 44796.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077548 restraints weight = 25769.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077992 restraints weight = 23255.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078117 restraints weight = 22729.413| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30489 Z= 0.204 Angle : 0.675 17.908 41622 Z= 0.327 Chirality : 0.046 0.349 4893 Planarity : 0.005 0.067 5277 Dihedral : 4.861 28.439 3960 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.62 % Favored : 89.35 % Rotamer: Outliers : 2.16 % Allowed : 16.03 % Favored : 81.82 % 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: -1.74 (0.13), residues: 3663 helix: 0.76 (0.17), residues: 957 sheet: -0.80 (0.19), residues: 741 loop : -2.38 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 457 TYR 0.023 0.001 TYR E 473 PHE 0.018 0.002 PHE A 157 TRP 0.012 0.001 TRP A 152 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (30381) covalent geometry : angle 0.64809 / 0.32 (41340) SS BOND : bond 0.00400 / 0.24 ( 42) SS BOND : angle 1.72633 / 1.02 ( 84) hydrogen bonds : bond 0.04795 / 3.11 ( 999) hydrogen bonds : angle 5.06509 / 3.51 ( 2799) link_ALPHA1-3 : bond 0.00710 / 0.35 ( 3) link_ALPHA1-3 : angle 1.75744 / 1.05 ( 9) link_BETA1-4 : bond 0.01012 / 0.74 ( 27) link_BETA1-4 : angle 2.63770 / 1.96 ( 81) link_NAG-ASN : bond 0.00437 / 0.26 ( 36) link_NAG-ASN : angle 2.64865 / 1.84 ( 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 194 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7011 (t0) cc_final: 0.6582 (m-40) REVERT: A 731 MET cc_start: 0.9170 (ptt) cc_final: 0.8908 (ptt) REVERT: C 84 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (mm) REVERT: C 425 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7484 (tp) REVERT: C 554 GLU cc_start: 0.7625 (mp0) cc_final: 0.7416 (mp0) REVERT: D 147 LYS cc_start: 0.4094 (mmtm) cc_final: 0.3780 (mttm) REVERT: E 137 ASN cc_start: 0.7032 (t0) cc_final: 0.6629 (m-40) REVERT: E 329 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8668 (t80) REVERT: E 633 TRP cc_start: 0.6173 (OUTLIER) cc_final: 0.5820 (p90) outliers start: 69 outliers final: 53 residues processed: 187 average time/residue: 0.1469 time to fit residues: 48.3827 Evaluate side-chains 177 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS 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 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 18 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 125 ASN 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 425 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1027 THR 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 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 464 PHE 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 599 THR Chi-restraints excluded: chain E residue 633 TRP 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 E residue 1027 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 329 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.121084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.076809 restraints weight = 83158.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080187 restraints weight = 41273.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079878 restraints weight = 23568.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080338 restraints weight = 21324.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080539 restraints weight = 20995.964| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30489 Z= 0.118 Angle : 0.630 17.889 41622 Z= 0.303 Chirality : 0.045 0.353 4893 Planarity : 0.004 0.066 5277 Dihedral : 4.671 26.539 3960 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 1.66 % Allowed : 16.74 % Favored : 81.60 % 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: 1.04 (0.17), residues: 957 sheet: -0.70 (0.19), residues: 738 loop : -2.24 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 457 TYR 0.024 0.001 TYR C 473 PHE 0.019 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (30381) covalent geometry : angle 0.60408 / 0.30 (41340) SS BOND : bond 0.00277 / 0.17 ( 42) SS BOND : angle 1.51248 / 0.96 ( 84) hydrogen bonds : bond 0.03976 / 2.58 ( 999) hydrogen bonds : angle 4.81314 / 3.33 ( 2799) link_ALPHA1-3 : bond 0.00798 / 0.40 ( 3) link_ALPHA1-3 : angle 1.55031 / 0.94 ( 9) link_BETA1-4 : bond 0.01021 / 0.75 ( 27) link_BETA1-4 : angle 2.59208 / 1.92 ( 81) link_NAG-ASN : bond 0.00421 / 0.26 ( 36) link_NAG-ASN : angle 2.50775 / 1.76 ( 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 192 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.6978 (t0) cc_final: 0.6536 (m-40) REVERT: A 731 MET cc_start: 0.8956 (ptt) cc_final: 0.8667 (ptt) REVERT: C 84 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (mm) REVERT: C 554 GLU cc_start: 0.7606 (mp0) cc_final: 0.7386 (mp0) REVERT: D 147 LYS cc_start: 0.4086 (mmtm) cc_final: 0.3738 (mttm) REVERT: E 137 ASN cc_start: 0.6887 (t0) cc_final: 0.6404 (m-40) outliers start: 53 outliers final: 41 residues processed: 187 average time/residue: 0.1611 time to fit residues: 51.6279 Evaluate side-chains 166 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS 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 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 18 LEU Chi-restraints excluded: chain B residue 60 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 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 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 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 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 22 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.119501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075139 restraints weight = 82798.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078406 restraints weight = 42651.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.078244 restraints weight = 24065.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078520 restraints weight = 20636.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078651 restraints weight = 21694.724| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30489 Z= 0.193 Angle : 0.669 17.822 41622 Z= 0.323 Chirality : 0.046 0.353 4893 Planarity : 0.005 0.079 5277 Dihedral : 4.786 27.348 3960 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.35 % Favored : 89.63 % Rotamer: Outliers : 1.59 % Allowed : 17.03 % Favored : 81.38 % 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: -1.59 (0.14), residues: 3663 helix: 0.92 (0.17), residues: 957 sheet: -0.82 (0.19), residues: 756 loop : -2.27 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 454 TYR 0.022 0.001 TYR C 473 PHE 0.015 0.001 PHE A 157 TRP 0.040 0.002 TRP E 353 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (30381) covalent geometry : angle 0.64304 / 0.32 (41340) SS BOND : bond 0.00384 / 0.23 ( 42) SS BOND : angle 1.72150 / 1.07 ( 84) hydrogen bonds : bond 0.04581 / 2.96 ( 999) hydrogen bonds : angle 4.92352 / 3.41 ( 2799) link_ALPHA1-3 : bond 0.00682 / 0.34 ( 3) link_ALPHA1-3 : angle 1.62791 / 0.99 ( 9) link_BETA1-4 : bond 0.00998 / 0.73 ( 27) link_BETA1-4 : angle 2.61442 / 1.95 ( 81) link_NAG-ASN : bond 0.00402 / 0.24 ( 36) link_NAG-ASN : angle 2.56070 / 1.77 ( 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 173 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7058 (t0) cc_final: 0.6629 (m-40) REVERT: A 731 MET cc_start: 0.9166 (ptt) cc_final: 0.8910 (ptt) REVERT: C 84 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8146 (mm) REVERT: C 554 GLU cc_start: 0.7623 (mp0) cc_final: 0.7404 (mp0) REVERT: D 147 LYS cc_start: 0.4158 (mmtm) cc_final: 0.3805 (mttm) REVERT: E 137 ASN cc_start: 0.7043 (t0) cc_final: 0.6648 (m-40) outliers start: 51 outliers final: 45 residues processed: 169 average time/residue: 0.1677 time to fit residues: 49.4193 Evaluate side-chains 165 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS 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 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 18 LEU Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 60 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 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 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 318 PHE Chi-restraints excluded: chain E residue 439 ASN 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 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 303 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 187 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 312 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.119755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075449 restraints weight = 83093.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.078600 restraints weight = 43223.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078459 restraints weight = 24768.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078787 restraints weight = 21016.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078809 restraints weight = 22182.218| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30489 Z= 0.169 Angle : 0.660 17.987 41622 Z= 0.318 Chirality : 0.045 0.355 4893 Planarity : 0.005 0.078 5277 Dihedral : 4.782 27.857 3960 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.64 % Favored : 90.34 % Rotamer: Outliers : 1.66 % Allowed : 17.18 % Favored : 81.16 % 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: -1.58 (0.14), residues: 3663 helix: 0.93 (0.17), residues: 957 sheet: -0.82 (0.19), residues: 756 loop : -2.27 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 457 TYR 0.023 0.001 TYR C 473 PHE 0.016 0.001 PHE A 157 TRP 0.029 0.001 TRP E 353 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (30381) covalent geometry : angle 0.63391 / 0.31 (41340) SS BOND : bond 0.00363 / 0.22 ( 42) SS BOND : angle 1.64548 / 1.01 ( 84) hydrogen bonds : bond 0.04444 / 2.88 ( 999) hydrogen bonds : angle 4.90045 / 3.39 ( 2799) link_ALPHA1-3 : bond 0.00685 / 0.34 ( 3) link_ALPHA1-3 : angle 1.60205 / 0.98 ( 9) link_BETA1-4 : bond 0.01034 / 0.76 ( 27) link_BETA1-4 : angle 2.62008 / 1.95 ( 81) link_NAG-ASN : bond 0.00391 / 0.24 ( 36) link_NAG-ASN : angle 2.54213 / 1.77 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.89 seconds wall clock time: 95 minutes 24.24 seconds (5724.24 seconds total)