Starting phenix.real_space_refine on Fri Mar 6 01:42:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwy_30889/03_2026/7dwy_30889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwy_30889/03_2026/7dwy_30889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dwy_30889/03_2026/7dwy_30889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwy_30889/03_2026/7dwy_30889.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwy_30889/03_2026/7dwy_30889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwy_30889/03_2026/7dwy_30889_neut.cif" } resolution = 2.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17151 2.51 5 N 4389 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26979 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 286 Unusual residues: {'EIC': 1, 'NAG': 19} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "B" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 314 Unusual residues: {'EIC': 1, 'NAG': 21} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 286 Unusual residues: {'EIC': 1, 'NAG': 19} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 5.44, per 1000 atoms: 0.20 Number of scatterers: 26979 At special positions: 0 Unit cell: (145.658, 146.745, 169.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5319 8.00 N 4389 7.00 C 17151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.78 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.48 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.49 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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 A 840 " - pdb=" SG CYS A 851 " 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 B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.78 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.48 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.49 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=1.78 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.48 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=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1401 " - " NAG A1402 " " NAG A1409 " - " NAG A1410 " " NAG A1412 " - " NAG A1413 " " NAG A1416 " - " NAG A1417 " " NAG A1418 " - " NAG A1419 " " NAG B1401 " - " NAG B1402 " " NAG B1409 " - " NAG B1410 " " NAG B1412 " - " NAG B1413 " " NAG B1416 " - " NAG B1417 " " NAG B1418 " - " NAG B1419 " " NAG B1420 " - " NAG B1421 " " NAG C1401 " - " NAG C1402 " " NAG C1410 " - " NAG C1411 " " NAG C1414 " - " NAG C1415 " " NAG C1416 " - " NAG C1417 " " NAG C1418 " - " NAG C1419 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1401 " - " ASN A 17 " " NAG A1403 " - " ASN A 61 " " NAG A1404 " - " ASN A 122 " " NAG A1405 " - " ASN A 149 " " NAG A1406 " - " ASN A 165 " " NAG A1407 " - " ASN A 234 " " NAG A1408 " - " ASN A 282 " " NAG A1409 " - " ASN A 343 " " NAG A1411 " - " ASN A 603 " " NAG A1412 " - " ASN A 616 " " NAG A1414 " - " ASN A 657 " " NAG A1415 " - " ASN A 709 " " NAG A1416 " - " ASN A 801 " " NAG A1418 " - " ASN A1134 " " NAG B1401 " - " ASN B 17 " " NAG B1403 " - " ASN B 61 " " NAG B1404 " - " ASN B 122 " " NAG B1405 " - " ASN B 149 " " NAG B1406 " - " ASN B 165 " " NAG B1407 " - " ASN B 234 " " NAG B1408 " - " ASN B 282 " " NAG B1409 " - " ASN B 343 " " NAG B1411 " - " ASN B 603 " " NAG B1412 " - " ASN B 616 " " NAG B1414 " - " ASN B 657 " " NAG B1415 " - " ASN B 709 " " NAG B1416 " - " ASN B 801 " " NAG B1418 " - " ASN B1074 " " NAG B1420 " - " ASN B1134 " " NAG C1401 " - " ASN C 17 " " NAG C1403 " - " ASN C 61 " " NAG C1404 " - " ASN C 122 " " NAG C1405 " - " ASN C 149 " " NAG C1406 " - " ASN C 165 " " NAG C1407 " - " ASN C 234 " " NAG C1408 " - " ASN C 282 " " NAG C1409 " - " ASN C 603 " " NAG C1410 " - " ASN C 616 " " NAG C1412 " - " ASN C 657 " " NAG C1413 " - " ASN C 709 " " NAG C1414 " - " ASN C 801 " " NAG C1416 " - " ASN C1074 " " NAG C1418 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN C 331 " " NAG L 1 " - " ASN C 343 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 23.4% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.682A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.503A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.744A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 841 removed outlier: 4.058A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.099A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.945A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.682A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.682A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.504A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.744A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 841 removed outlier: 4.058A pdb=" N LEU B 841 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.099A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.682A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.682A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.503A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.745A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 841 removed outlier: 4.059A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.099A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.944A 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.208A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.485A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.930A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.153A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.490A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.963A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.208A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.485A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.930A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.656A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.153A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.491A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 7.125A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.207A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.485A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.930A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.152A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.490A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.576A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.576A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1089 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.75 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8394 1.33 - 1.46: 6351 1.46 - 1.58: 12681 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 27576 Sorted by residual: bond pdb=" C1 NAG B1410 " pdb=" C2 NAG B1410 " ideal model delta sigma weight residual 1.532 1.418 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C1 NAG A1410 " pdb=" C2 NAG A1410 " ideal model delta sigma weight residual 1.532 1.418 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C1 NAG L 2 " pdb=" C2 NAG L 2 " ideal model delta sigma weight residual 1.532 1.418 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.302 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.303 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 27571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 35377 1.67 - 3.34: 1764 3.34 - 5.01: 288 5.01 - 6.67: 43 6.67 - 8.34: 31 Bond angle restraints: 37503 Sorted by residual: angle pdb=" N ARG B 847 " pdb=" CA ARG B 847 " pdb=" C ARG B 847 " ideal model delta sigma weight residual 114.56 107.64 6.92 1.27e+00 6.20e-01 2.97e+01 angle pdb=" N ARG C 847 " pdb=" CA ARG C 847 " pdb=" C ARG C 847 " ideal model delta sigma weight residual 114.56 107.68 6.88 1.27e+00 6.20e-01 2.94e+01 angle pdb=" N ARG A 847 " pdb=" CA ARG A 847 " pdb=" C ARG A 847 " ideal model delta sigma weight residual 114.56 107.70 6.86 1.27e+00 6.20e-01 2.92e+01 angle pdb=" CA GLN C1142 " pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 120.79 116.42 4.37 9.70e-01 1.06e+00 2.03e+01 angle pdb=" CA GLN B1142 " pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 120.79 116.45 4.34 9.70e-01 1.06e+00 2.00e+01 ... (remaining 37498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 15163 17.54 - 35.09: 1478 35.09 - 52.63: 563 52.63 - 70.17: 231 70.17 - 87.72: 37 Dihedral angle restraints: 17472 sinusoidal: 7881 harmonic: 9591 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.58 80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 17469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 4412 0.304 - 0.609: 16 0.609 - 0.913: 12 0.913 - 1.218: 12 1.218 - 1.522: 9 Chirality restraints: 4461 Sorted by residual: chirality pdb=" C1 NAG B1413 " pdb=" O4 NAG B1412 " pdb=" C2 NAG B1413 " pdb=" O5 NAG B1413 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG A1413 " pdb=" O4 NAG A1412 " pdb=" C2 NAG A1413 " pdb=" O5 NAG A1413 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 ... (remaining 4458 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN B 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG B1414 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG A1414 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN C 657 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.577 2.00e-02 2.50e+03 pdb=" C1 NAG C1412 " -0.391 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 148 2.51 - 3.11: 18678 3.11 - 3.70: 37232 3.70 - 4.30: 58748 4.30 - 4.90: 99534 Nonbonded interactions: 214340 Sorted by model distance: nonbonded pdb=" O SER B 940 " pdb=" OG1 THR B 941 " model vdw 1.911 3.040 nonbonded pdb=" O SER A 940 " pdb=" OG1 THR A 941 " model vdw 1.911 3.040 nonbonded pdb=" O SER C 940 " pdb=" OG1 THR C 941 " model vdw 1.911 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.195 3.040 ... (remaining 214335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1419) selection = (chain 'B' and resid 14 through 1419) selection = (chain 'C' and resid 14 through 1419) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.920 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.013 0.457 27702 Z= 0.634 Angle : 1.682 58.505 37836 Z= 0.698 Chirality : 0.110 1.522 4461 Planarity : 0.011 0.279 4755 Dihedral : 17.257 87.718 11175 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.42 % Favored : 94.21 % Rotamer: Outliers : 12.02 % Allowed : 13.34 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.12), residues: 3267 helix: -0.88 (0.18), residues: 714 sheet: -0.12 (0.18), residues: 765 loop : -2.88 (0.11), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.023 0.002 TYR B 756 PHE 0.016 0.002 PHE A 133 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00880 (27576) covalent geometry : angle 0.85969 (37503) SS BOND : bond 0.17745 ( 45) SS BOND : angle 11.14045 ( 90) hydrogen bonds : bond 0.12611 ( 1047) hydrogen bonds : angle 7.12976 ( 2970) link_BETA1-4 : bond 0.20532 ( 27) link_BETA1-4 : angle 15.21224 ( 81) link_NAG-ASN : bond 0.07010 ( 54) link_NAG-ASN : angle 17.46717 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 345 poor density : 352 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 66 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6450 (p-80) REVERT: A 208 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8151 (p) REVERT: A 471 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: B 185 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5799 (t0) REVERT: B 212 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6478 (tp) REVERT: B 900 MET cc_start: 0.8728 (mtp) cc_final: 0.8483 (mtm) REVERT: C 66 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6668 (p-80) REVERT: C 212 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (tm) REVERT: C 258 TRP cc_start: 0.8542 (p-90) cc_final: 0.8253 (p-90) REVERT: C 259 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8196 (m) REVERT: C 462 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8305 (mmtt) REVERT: C 606 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7599 (p0) outliers start: 345 outliers final: 46 residues processed: 609 average time/residue: 0.5026 time to fit residues: 366.1162 Evaluate side-chains 248 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 4.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 207 HIS A 239 GLN A 314 GLN A 317 ASN A 448 ASN A 450 ASN A 532 ASN A 544 ASN A 556 ASN A 564 GLN A 606 ASN A 613 GLN A 644 GLN A 751 ASN A 804 GLN A 919 ASN A 925 ASN A1010 GLN A1023 ASN A1036 GLN A1054 GLN A1064 HIS B 207 HIS B 239 GLN B 314 GLN B 317 ASN B 440 ASN B 448 ASN B 450 ASN B 498 GLN B 544 ASN B 556 ASN B 564 GLN B 613 GLN B 644 GLN B 751 ASN B 919 ASN B 925 ASN B1023 ASN B1036 GLN B1054 GLN B1064 HIS C 121 ASN C 185 ASN C 207 HIS C 239 GLN C 314 GLN C 317 ASN C 440 ASN C 448 ASN C 450 ASN C 498 GLN C 544 ASN C 556 ASN C 564 GLN C 613 GLN C 644 GLN C 751 ASN C 919 ASN C 925 ASN C1023 ASN C1036 GLN C1054 GLN C1064 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098145 restraints weight = 36944.122| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.46 r_work: 0.3109 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27702 Z= 0.129 Angle : 0.782 11.832 37836 Z= 0.355 Chirality : 0.054 0.784 4461 Planarity : 0.004 0.044 4755 Dihedral : 9.463 80.827 5368 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.59 % Allowed : 18.29 % Favored : 78.13 % 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: -1.62 (0.13), residues: 3267 helix: 0.53 (0.20), residues: 699 sheet: 0.49 (0.19), residues: 720 loop : -2.53 (0.11), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 567 TYR 0.017 0.001 TYR C 837 PHE 0.013 0.001 PHE C 592 TRP 0.011 0.001 TRP C 152 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00274 (27576) covalent geometry : angle 0.67590 (37503) SS BOND : bond 0.00578 ( 45) SS BOND : angle 1.84867 ( 90) hydrogen bonds : bond 0.04924 ( 1047) hydrogen bonds : angle 5.63069 ( 2970) link_BETA1-4 : bond 0.00518 ( 27) link_BETA1-4 : angle 2.87086 ( 81) link_NAG-ASN : bond 0.00739 ( 54) link_NAG-ASN : angle 5.55808 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 232 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6216 (p-80) REVERT: A 208 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7907 (p) REVERT: A 574 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8188 (p0) REVERT: A 603 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8041 (t0) REVERT: A 776 LYS cc_start: 0.8668 (tttt) cc_final: 0.8425 (tttm) REVERT: A 979 ASP cc_start: 0.7780 (m-30) cc_final: 0.7325 (OUTLIER) REVERT: A 1002 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7889 (tp-100) REVERT: A 1141 LEU cc_start: 0.8316 (tp) cc_final: 0.8002 (tm) REVERT: A 1142 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: B 66 HIS cc_start: 0.6642 (OUTLIER) cc_final: 0.5824 (p-80) REVERT: B 185 ASN cc_start: 0.5834 (OUTLIER) cc_final: 0.5227 (t0) REVERT: B 197 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 212 LEU cc_start: 0.6544 (tp) cc_final: 0.6127 (tp) REVERT: B 900 MET cc_start: 0.9064 (mtp) cc_final: 0.8822 (mtm) REVERT: C 177 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7997 (ttp) REVERT: C 259 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7625 (m) REVERT: C 462 LYS cc_start: 0.8797 (mmtp) cc_final: 0.8473 (mmtt) REVERT: C 606 ASN cc_start: 0.7940 (m-40) cc_final: 0.7350 (p0) REVERT: C 646 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8377 (mtm-85) REVERT: C 940 SER cc_start: 0.7754 (t) cc_final: 0.7464 (m) REVERT: C 979 ASP cc_start: 0.7840 (m-30) cc_final: 0.7581 (t0) outliers start: 103 outliers final: 37 residues processed: 317 average time/residue: 0.5107 time to fit residues: 193.1886 Evaluate side-chains 227 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 175 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 388 ASN A 501 ASN A 606 ASN A 935 GLN A1125 ASN B 641 ASN B 804 GLN B 856 ASN B1083 HIS B1125 ASN C 188 ASN C1142 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093436 restraints weight = 37652.544| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.42 r_work: 0.3029 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 27702 Z= 0.256 Angle : 0.802 14.181 37836 Z= 0.380 Chirality : 0.054 0.543 4461 Planarity : 0.005 0.041 4755 Dihedral : 8.442 80.634 5312 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.11 % Allowed : 18.01 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.13), residues: 3267 helix: 0.57 (0.20), residues: 714 sheet: 0.56 (0.19), residues: 729 loop : -2.42 (0.11), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.020 0.002 TYR A 756 PHE 0.020 0.002 PHE B 759 TRP 0.012 0.002 TRP B 152 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00635 (27576) covalent geometry : angle 0.73075 (37503) SS BOND : bond 0.00778 ( 45) SS BOND : angle 2.17381 ( 90) hydrogen bonds : bond 0.06136 ( 1047) hydrogen bonds : angle 5.63374 ( 2970) link_BETA1-4 : bond 0.00461 ( 27) link_BETA1-4 : angle 2.73313 ( 81) link_NAG-ASN : bond 0.00547 ( 54) link_NAG-ASN : angle 4.48823 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 189 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6662 (p-80) REVERT: A 78 ARG cc_start: 0.6283 (mmm160) cc_final: 0.6058 (mmt180) REVERT: A 346 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7699 (ttm-80) REVERT: A 574 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 776 LYS cc_start: 0.8786 (tttt) cc_final: 0.8493 (tttm) REVERT: A 916 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 979 ASP cc_start: 0.8053 (m-30) cc_final: 0.7698 (t0) REVERT: A 1002 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7976 (tp-100) REVERT: A 1005 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: B 66 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6057 (p-80) REVERT: B 151 SER cc_start: 0.6976 (m) cc_final: 0.6749 (m) REVERT: B 185 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5459 (m-40) REVERT: B 212 LEU cc_start: 0.6568 (tp) cc_final: 0.6325 (tp) REVERT: B 606 ASN cc_start: 0.8391 (m-40) cc_final: 0.8112 (m110) REVERT: B 900 MET cc_start: 0.9098 (mtp) cc_final: 0.8861 (mtm) REVERT: C 216 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7538 (tp) REVERT: C 223 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 259 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7714 (m) REVERT: C 462 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8647 (mmtt) REVERT: C 606 ASN cc_start: 0.7963 (m-40) cc_final: 0.7241 (p0) REVERT: C 646 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8160 (ttp80) REVERT: C 954 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: C 1002 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8242 (tm-30) outliers start: 118 outliers final: 47 residues processed: 283 average time/residue: 0.4988 time to fit residues: 168.9340 Evaluate side-chains 227 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 229 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 606 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096668 restraints weight = 37372.919| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.42 r_work: 0.3084 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27702 Z= 0.126 Angle : 0.642 10.410 37836 Z= 0.306 Chirality : 0.048 0.472 4461 Planarity : 0.004 0.040 4755 Dihedral : 7.644 95.993 5300 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.89 % Allowed : 18.88 % Favored : 78.23 % 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: -1.09 (0.14), residues: 3267 helix: 1.09 (0.20), residues: 714 sheet: 0.85 (0.20), residues: 666 loop : -2.20 (0.12), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.017 0.001 TYR C 837 PHE 0.012 0.001 PHE B 759 TRP 0.012 0.001 TRP B 152 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00291 (27576) covalent geometry : angle 0.59355 (37503) SS BOND : bond 0.00580 ( 45) SS BOND : angle 1.47616 ( 90) hydrogen bonds : bond 0.04527 ( 1047) hydrogen bonds : angle 5.23578 ( 2970) link_BETA1-4 : bond 0.00487 ( 27) link_BETA1-4 : angle 2.16688 ( 81) link_NAG-ASN : bond 0.00349 ( 54) link_NAG-ASN : angle 3.32022 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 193 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6313 (mmm160) cc_final: 0.6022 (mmt180) REVERT: A 346 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7649 (ttm-80) REVERT: A 574 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8150 (p0) REVERT: A 776 LYS cc_start: 0.8713 (tttt) cc_final: 0.8402 (tttm) REVERT: A 979 ASP cc_start: 0.7745 (m-30) cc_final: 0.7545 (t0) REVERT: A 988 GLU cc_start: 0.8235 (pm20) cc_final: 0.7902 (pm20) REVERT: A 1002 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7916 (tp-100) REVERT: B 66 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6096 (p-80) REVERT: B 185 ASN cc_start: 0.5991 (OUTLIER) cc_final: 0.5620 (m-40) REVERT: B 281 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7796 (pp20) REVERT: B 324 GLU cc_start: 0.8030 (pt0) cc_final: 0.7812 (pm20) REVERT: B 519 HIS cc_start: 0.7966 (m-70) cc_final: 0.7639 (t-90) REVERT: B 606 ASN cc_start: 0.8053 (m-40) cc_final: 0.7831 (m110) REVERT: B 763 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 900 MET cc_start: 0.9080 (mtp) cc_final: 0.8864 (mtm) REVERT: C 153 MET cc_start: 0.7553 (tpp) cc_final: 0.7044 (mtp) REVERT: C 180 GLU cc_start: 0.8070 (tt0) cc_final: 0.7758 (tm-30) REVERT: C 212 LEU cc_start: 0.7485 (tp) cc_final: 0.7026 (tm) REVERT: C 259 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7593 (m) REVERT: C 462 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8564 (mmtt) REVERT: C 606 ASN cc_start: 0.7847 (m-40) cc_final: 0.7074 (p0) REVERT: C 646 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8260 (mtp85) REVERT: C 988 GLU cc_start: 0.8381 (tp30) cc_final: 0.8063 (tp30) REVERT: C 1005 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8407 (mt0) outliers start: 83 outliers final: 29 residues processed: 262 average time/residue: 0.5517 time to fit residues: 171.1616 Evaluate side-chains 213 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 23 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 218 GLN B 644 GLN B1002 GLN B1005 GLN C 644 GLN C 751 ASN C 764 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092920 restraints weight = 37681.884| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.40 r_work: 0.3024 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 27702 Z= 0.248 Angle : 0.746 16.444 37836 Z= 0.361 Chirality : 0.052 0.395 4461 Planarity : 0.004 0.049 4755 Dihedral : 7.648 100.546 5295 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.83 % Allowed : 18.25 % Favored : 77.92 % 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: -1.15 (0.14), residues: 3267 helix: 0.90 (0.20), residues: 714 sheet: 0.77 (0.19), residues: 705 loop : -2.21 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.019 0.002 TYR A 756 PHE 0.017 0.002 PHE A 898 TRP 0.010 0.002 TRP B 152 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00619 (27576) covalent geometry : angle 0.69595 (37503) SS BOND : bond 0.00719 ( 45) SS BOND : angle 2.63782 ( 90) hydrogen bonds : bond 0.05916 ( 1047) hydrogen bonds : angle 5.48441 ( 2970) link_BETA1-4 : bond 0.00414 ( 27) link_BETA1-4 : angle 2.17504 ( 81) link_NAG-ASN : bond 0.00372 ( 54) link_NAG-ASN : angle 3.43289 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 183 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6577 (mmm160) cc_final: 0.6308 (mmt180) REVERT: A 574 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8161 (p0) REVERT: A 675 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: A 776 LYS cc_start: 0.8793 (tttt) cc_final: 0.8468 (tttm) REVERT: A 979 ASP cc_start: 0.7960 (m-30) cc_final: 0.7713 (t0) REVERT: A 1002 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8015 (tp-100) REVERT: B 66 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6016 (p-80) REVERT: B 96 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 185 ASN cc_start: 0.6262 (OUTLIER) cc_final: 0.5893 (m-40) REVERT: B 281 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: B 324 GLU cc_start: 0.8077 (pt0) cc_final: 0.7876 (pm20) REVERT: B 519 HIS cc_start: 0.8076 (m-70) cc_final: 0.7620 (t-90) REVERT: B 554 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: B 900 MET cc_start: 0.9094 (mtp) cc_final: 0.8850 (mtm) REVERT: C 153 MET cc_start: 0.7635 (tpp) cc_final: 0.6982 (mtp) REVERT: C 180 GLU cc_start: 0.8152 (tt0) cc_final: 0.7915 (tt0) REVERT: C 462 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8619 (mmtt) REVERT: C 606 ASN cc_start: 0.7789 (m-40) cc_final: 0.6935 (p0) REVERT: C 646 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8180 (ttp80) REVERT: C 983 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8282 (ptm160) REVERT: C 988 GLU cc_start: 0.8406 (tp30) cc_final: 0.8193 (tp30) REVERT: C 1005 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8441 (mt0) outliers start: 110 outliers final: 46 residues processed: 270 average time/residue: 0.5577 time to fit residues: 177.4432 Evaluate side-chains 230 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 16 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 241 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A1005 GLN B1005 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096563 restraints weight = 37208.324| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.39 r_work: 0.3082 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27702 Z= 0.112 Angle : 0.638 17.657 37836 Z= 0.307 Chirality : 0.047 0.485 4461 Planarity : 0.004 0.046 4755 Dihedral : 7.318 106.738 5294 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.58 % Allowed : 19.64 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3267 helix: 1.32 (0.20), residues: 714 sheet: 0.82 (0.20), residues: 672 loop : -2.05 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.017 0.001 TYR C1067 PHE 0.011 0.001 PHE A1121 TRP 0.011 0.001 TRP B 152 HIS 0.003 0.000 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00252 (27576) covalent geometry : angle 0.59329 (37503) SS BOND : bond 0.00613 ( 45) SS BOND : angle 2.27709 ( 90) hydrogen bonds : bond 0.04448 ( 1047) hydrogen bonds : angle 5.16585 ( 2970) link_BETA1-4 : bond 0.00445 ( 27) link_BETA1-4 : angle 1.89348 ( 81) link_NAG-ASN : bond 0.00384 ( 54) link_NAG-ASN : angle 3.00892 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6528 (mmm160) cc_final: 0.6268 (mmt180) REVERT: A 158 ARG cc_start: 0.6158 (mmm-85) cc_final: 0.5377 (mmt90) REVERT: A 346 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: A 776 LYS cc_start: 0.8727 (tttt) cc_final: 0.8424 (tttm) REVERT: A 988 GLU cc_start: 0.8346 (pm20) cc_final: 0.8036 (pm20) REVERT: A 1002 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8015 (tp-100) REVERT: B 66 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6255 (p-80) REVERT: B 96 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 519 HIS cc_start: 0.7983 (m-70) cc_final: 0.7621 (t-90) REVERT: B 554 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: B 571 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8059 (t0) REVERT: B 661 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: B 900 MET cc_start: 0.9097 (mtp) cc_final: 0.8870 (mtm) REVERT: C 153 MET cc_start: 0.7623 (tpp) cc_final: 0.6881 (mtp) REVERT: C 462 LYS cc_start: 0.8888 (mmtp) cc_final: 0.8587 (mmtt) REVERT: C 606 ASN cc_start: 0.7757 (m-40) cc_final: 0.6879 (p0) REVERT: C 988 GLU cc_start: 0.8349 (tp30) cc_final: 0.8001 (tp30) REVERT: C 1005 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8409 (mt0) outliers start: 74 outliers final: 38 residues processed: 247 average time/residue: 0.5781 time to fit residues: 167.8038 Evaluate side-chains 212 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 24 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 294 optimal weight: 0.8980 chunk 309 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 302 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 360 ASN A1005 GLN B1005 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097893 restraints weight = 37178.909| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.39 r_work: 0.3104 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27702 Z= 0.107 Angle : 0.611 18.909 37836 Z= 0.294 Chirality : 0.046 0.318 4461 Planarity : 0.004 0.043 4755 Dihedral : 7.082 111.674 5292 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.72 % Allowed : 19.82 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3267 helix: 1.58 (0.20), residues: 714 sheet: 0.86 (0.20), residues: 687 loop : -1.94 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 357 TYR 0.017 0.001 TYR A1067 PHE 0.011 0.001 PHE B 32 TRP 0.010 0.001 TRP B 152 HIS 0.004 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00240 (27576) covalent geometry : angle 0.57406 (37503) SS BOND : bond 0.00665 ( 45) SS BOND : angle 1.97867 ( 90) hydrogen bonds : bond 0.04105 ( 1047) hydrogen bonds : angle 4.98276 ( 2970) link_BETA1-4 : bond 0.00452 ( 27) link_BETA1-4 : angle 1.75975 ( 81) link_NAG-ASN : bond 0.00362 ( 54) link_NAG-ASN : angle 2.69220 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 179 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6518 (mmm160) cc_final: 0.6268 (mmt180) REVERT: A 158 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5388 (mmt90) REVERT: A 346 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7454 (ttm-80) REVERT: A 776 LYS cc_start: 0.8674 (tttt) cc_final: 0.8433 (tttm) REVERT: A 936 ASP cc_start: 0.7336 (t0) cc_final: 0.6857 (m-30) REVERT: A 988 GLU cc_start: 0.8341 (pm20) cc_final: 0.7998 (pm20) REVERT: A 1002 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7990 (tp-100) REVERT: B 66 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6279 (p-80) REVERT: B 88 ASP cc_start: 0.8628 (m-30) cc_final: 0.8262 (m-30) REVERT: B 173 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: B 519 HIS cc_start: 0.8025 (m-70) cc_final: 0.7642 (t-90) REVERT: B 554 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: B 571 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8031 (t0) REVERT: B 763 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 153 MET cc_start: 0.7570 (tpp) cc_final: 0.6810 (mtp) REVERT: C 462 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8544 (mmtt) REVERT: C 606 ASN cc_start: 0.7749 (m-40) cc_final: 0.6887 (p0) REVERT: C 780 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: C 988 GLU cc_start: 0.8327 (tp30) cc_final: 0.8023 (tp30) REVERT: C 1005 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8467 (mt0) outliers start: 78 outliers final: 37 residues processed: 243 average time/residue: 0.5402 time to fit residues: 156.1453 Evaluate side-chains 211 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 311 optimal weight: 0.5980 chunk 319 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A1119 ASN B1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095727 restraints weight = 37558.446| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.42 r_work: 0.3069 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27702 Z= 0.150 Angle : 0.639 18.539 37836 Z= 0.310 Chirality : 0.048 0.306 4461 Planarity : 0.004 0.043 4755 Dihedral : 7.026 110.517 5291 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.44 % Allowed : 20.20 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3267 helix: 1.47 (0.20), residues: 714 sheet: 0.88 (0.20), residues: 672 loop : -1.94 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE C 592 TRP 0.009 0.001 TRP B 152 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00364 (27576) covalent geometry : angle 0.60251 (37503) SS BOND : bond 0.00550 ( 45) SS BOND : angle 2.20237 ( 90) hydrogen bonds : bond 0.04726 ( 1047) hydrogen bonds : angle 5.09746 ( 2970) link_BETA1-4 : bond 0.00407 ( 27) link_BETA1-4 : angle 1.72633 ( 81) link_NAG-ASN : bond 0.00316 ( 54) link_NAG-ASN : angle 2.69018 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6584 (mmm160) cc_final: 0.6275 (mmt180) REVERT: A 158 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5512 (mmt90) REVERT: A 216 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6951 (tp) REVERT: A 346 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7425 (ttm-80) REVERT: A 776 LYS cc_start: 0.8702 (tttt) cc_final: 0.8451 (tttm) REVERT: A 936 ASP cc_start: 0.7371 (t0) cc_final: 0.6912 (m-30) REVERT: A 988 GLU cc_start: 0.8335 (pm20) cc_final: 0.7972 (pm20) REVERT: A 1002 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8004 (tp-100) REVERT: B 66 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6307 (p-80) REVERT: B 88 ASP cc_start: 0.8588 (m-30) cc_final: 0.8213 (m-30) REVERT: B 173 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: B 519 HIS cc_start: 0.8062 (m-70) cc_final: 0.7658 (t-90) REVERT: B 554 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: B 571 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (t0) REVERT: B 661 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: B 763 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8531 (mt) REVERT: C 153 MET cc_start: 0.7339 (tpp) cc_final: 0.6670 (mtp) REVERT: C 173 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7675 (mm-40) REVERT: C 462 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8531 (mmtt) REVERT: C 606 ASN cc_start: 0.7785 (m-40) cc_final: 0.6898 (p0) REVERT: C 988 GLU cc_start: 0.8341 (tp30) cc_final: 0.8031 (tp30) REVERT: C 1005 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8390 (mt0) outliers start: 70 outliers final: 44 residues processed: 230 average time/residue: 0.5388 time to fit residues: 147.5518 Evaluate side-chains 217 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 144 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 153 optimal weight: 0.0270 chunk 304 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095472 restraints weight = 37603.134| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.40 r_work: 0.3067 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27702 Z= 0.168 Angle : 0.685 22.715 37836 Z= 0.328 Chirality : 0.050 0.485 4461 Planarity : 0.004 0.045 4755 Dihedral : 7.086 110.451 5291 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.61 % Allowed : 20.17 % Favored : 77.22 % Cbeta Deviations : 0.03 % 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: -0.78 (0.14), residues: 3267 helix: 1.40 (0.20), residues: 714 sheet: 0.87 (0.20), residues: 672 loop : -1.94 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.017 0.001 TYR C1067 PHE 0.014 0.001 PHE C 592 TRP 0.010 0.001 TRP B 152 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00409 (27576) covalent geometry : angle 0.62855 (37503) SS BOND : bond 0.00543 ( 45) SS BOND : angle 2.24796 ( 90) hydrogen bonds : bond 0.04887 ( 1047) hydrogen bonds : angle 5.14513 ( 2970) link_BETA1-4 : bond 0.00373 ( 27) link_BETA1-4 : angle 1.69979 ( 81) link_NAG-ASN : bond 0.00482 ( 54) link_NAG-ASN : angle 3.70416 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 169 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6602 (mmm160) cc_final: 0.6273 (mmt180) REVERT: A 158 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5521 (mmt90) REVERT: A 216 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7003 (tp) REVERT: A 346 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7445 (ttm-80) REVERT: A 776 LYS cc_start: 0.8724 (tttt) cc_final: 0.8421 (tttm) REVERT: A 936 ASP cc_start: 0.7405 (t0) cc_final: 0.6925 (m-30) REVERT: A 1002 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8029 (tp-100) REVERT: B 66 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6383 (p-80) REVERT: B 88 ASP cc_start: 0.8597 (m-30) cc_final: 0.8225 (m-30) REVERT: B 173 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: B 434 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 519 HIS cc_start: 0.8000 (m-70) cc_final: 0.7638 (t-90) REVERT: B 554 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: B 661 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: C 153 MET cc_start: 0.7356 (tpp) cc_final: 0.6662 (mtp) REVERT: C 173 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7687 (mm-40) REVERT: C 462 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8557 (mmtt) REVERT: C 606 ASN cc_start: 0.7755 (m-40) cc_final: 0.6987 (p0) REVERT: C 988 GLU cc_start: 0.8336 (tp30) cc_final: 0.8041 (tp30) REVERT: C 1005 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8407 (mt0) outliers start: 75 outliers final: 49 residues processed: 231 average time/residue: 0.5400 time to fit residues: 148.4927 Evaluate side-chains 223 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 99 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095229 restraints weight = 37538.740| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.39 r_work: 0.3061 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27702 Z= 0.168 Angle : 0.671 17.821 37836 Z= 0.323 Chirality : 0.048 0.402 4461 Planarity : 0.004 0.044 4755 Dihedral : 7.207 109.740 5291 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.26 % Allowed : 20.45 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3267 helix: 1.34 (0.20), residues: 717 sheet: 0.85 (0.20), residues: 672 loop : -1.93 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.018 0.001 TYR B 904 PHE 0.014 0.001 PHE C 592 TRP 0.010 0.001 TRP B 152 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00409 (27576) covalent geometry : angle 0.62604 (37503) SS BOND : bond 0.00521 ( 45) SS BOND : angle 2.26494 ( 90) hydrogen bonds : bond 0.04963 ( 1047) hydrogen bonds : angle 5.16789 ( 2970) link_BETA1-4 : bond 0.00363 ( 27) link_BETA1-4 : angle 1.64036 ( 81) link_NAG-ASN : bond 0.00357 ( 54) link_NAG-ASN : angle 3.19677 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 174 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6635 (mmm160) cc_final: 0.6315 (mmt180) REVERT: A 158 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5612 (mmt180) REVERT: A 216 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7072 (tp) REVERT: A 346 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7412 (ttm-80) REVERT: A 675 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: A 776 LYS cc_start: 0.8711 (tttt) cc_final: 0.8405 (tttm) REVERT: A 936 ASP cc_start: 0.7375 (t0) cc_final: 0.6909 (m-30) REVERT: A 1002 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8046 (tp-100) REVERT: B 66 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.6579 (p-80) REVERT: B 88 ASP cc_start: 0.8584 (m-30) cc_final: 0.8214 (m-30) REVERT: B 173 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: B 434 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8657 (mt) REVERT: B 519 HIS cc_start: 0.8001 (m-70) cc_final: 0.7645 (t-90) REVERT: B 554 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: B 661 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: C 153 MET cc_start: 0.7371 (tpp) cc_final: 0.6676 (mtp) REVERT: C 462 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8562 (mmtt) REVERT: C 606 ASN cc_start: 0.7759 (m-40) cc_final: 0.7029 (p0) REVERT: C 988 GLU cc_start: 0.8345 (tp30) cc_final: 0.8061 (tp30) REVERT: C 1005 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8388 (mt0) outliers start: 65 outliers final: 49 residues processed: 227 average time/residue: 0.5863 time to fit residues: 156.8039 Evaluate side-chains 226 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094911 restraints weight = 37234.042| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.36 r_work: 0.3058 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27702 Z= 0.171 Angle : 0.671 16.748 37836 Z= 0.325 Chirality : 0.048 0.361 4461 Planarity : 0.004 0.045 4755 Dihedral : 7.198 108.869 5291 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.37 % Allowed : 20.31 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3267 helix: 1.34 (0.20), residues: 717 sheet: 0.86 (0.20), residues: 672 loop : -1.93 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.018 0.001 TYR B 904 PHE 0.014 0.001 PHE C 592 TRP 0.010 0.001 TRP B 152 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00420 (27576) covalent geometry : angle 0.62708 (37503) SS BOND : bond 0.00579 ( 45) SS BOND : angle 2.26697 ( 90) hydrogen bonds : bond 0.05055 ( 1047) hydrogen bonds : angle 5.18344 ( 2970) link_BETA1-4 : bond 0.00352 ( 27) link_BETA1-4 : angle 1.57280 ( 81) link_NAG-ASN : bond 0.00281 ( 54) link_NAG-ASN : angle 3.16572 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8510.89 seconds wall clock time: 145 minutes 37.19 seconds (8737.19 seconds total)