Starting phenix.real_space_refine on Fri Mar 6 03:48:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nd8_12279/03_2026/7nd8_12279.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd8_12279/03_2026/7nd8_12279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nd8_12279/03_2026/7nd8_12279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd8_12279/03_2026/7nd8_12279.map" model { file = "/net/cci-nas-00/data/ceres_data/7nd8_12279/03_2026/7nd8_12279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd8_12279/03_2026/7nd8_12279.cif" } resolution = 3.5 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= 0.002 sd= 0.025 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 117 5.16 5 C 17579 2.51 5 N 4523 2.21 5 O 5440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 27659 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "L" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.71, per 1000 atoms: 0.21 Number of scatterers: 27659 At special positions: 0 Unit cell: (134.48, 162.36, 229.6, 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 117 16.00 O 5440 8.00 N 4523 7.00 C 17579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 208 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 916.4 milliseconds 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6446 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 58 sheets defined 23.5% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.564A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.388A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) 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 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.706A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.626A 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 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.111A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.870A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.608A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.531A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.402A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.716A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.611A 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 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.641A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.115A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.937A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.695A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.528A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.366A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) 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 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.721A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.656A 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 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.118A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.897A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 197 through 201 Processing helix chain 'H' and resid 213 through 216 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.638A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.603A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.106A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.794A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.584A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.350A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.351A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.068A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.347A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.545A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.016A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.536A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.530A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.029A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.879A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.224A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.345A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.007A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.332A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.215A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.408A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.548A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.548A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.655A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.960A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.337A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.547A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.981A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.485A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.693A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.693A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.550A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.789A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.768A pdb=" N ILE H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.973A pdb=" N TYR H 188 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.973A pdb=" N TYR H 188 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 163 through 166 removed outlier: 4.085A pdb=" N TYR H 206 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.980A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.307A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.242A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 153 through 154 1167 hydrogen bonds defined for protein. 3138 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: 6.86 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8787 1.34 - 1.46: 6976 1.46 - 1.58: 12355 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 28262 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 28257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 37818 2.35 - 4.71: 604 4.71 - 7.06: 23 7.06 - 9.41: 3 9.41 - 11.76: 3 Bond angle restraints: 38451 Sorted by residual: angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 122.66 -8.26 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA CYS B 760 " pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 114.40 122.44 -8.04 2.30e+00 1.89e-01 1.22e+01 angle pdb=" C GLU C 516 " pdb=" N LEU C 517 " pdb=" CA LEU C 517 " ideal model delta sigma weight residual 122.20 133.96 -11.76 3.42e+00 8.55e-02 1.18e+01 angle pdb=" C GLU A 516 " pdb=" N LEU A 517 " pdb=" CA LEU A 517 " ideal model delta sigma weight residual 122.20 133.76 -11.56 3.42e+00 8.55e-02 1.14e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 121.83 -7.43 2.30e+00 1.89e-01 1.04e+01 ... (remaining 38446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 16693 17.47 - 34.93: 672 34.93 - 52.40: 167 52.40 - 69.87: 66 69.87 - 87.33: 26 Dihedral angle restraints: 17624 sinusoidal: 7607 harmonic: 10017 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -166.15 80.15 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -164.04 78.04 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -162.82 76.82 1 1.00e+01 1.00e-02 7.41e+01 ... (remaining 17621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3087 0.041 - 0.082: 980 0.082 - 0.123: 445 0.123 - 0.164: 41 0.164 - 0.205: 4 Chirality restraints: 4557 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 4554 not shown) Planarity restraints: 4934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ALA C 958 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA C 958 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU C 959 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 954 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C GLN C 954 " -0.065 2.00e-02 2.50e+03 pdb=" O GLN C 954 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN C 955 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ALA A 958 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA A 958 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 959 " -0.022 2.00e-02 2.50e+03 ... (remaining 4931 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 803 2.70 - 3.25: 26360 3.25 - 3.80: 43843 3.80 - 4.35: 56982 4.35 - 4.90: 96203 Nonbonded interactions: 224191 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" OD1 ASN A 388 " model vdw 2.153 3.040 nonbonded pdb=" OG SER A1123 " pdb=" ND2 ASN B 914 " model vdw 2.193 3.120 nonbonded pdb=" OH TYR C 369 " pdb=" OD1 ASN C 388 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR B 369 " pdb=" OD1 ASN B 388 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.259 3.040 ... (remaining 224186 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' selection = (chain 'B' and resid 27 through 1309) selection = (chain 'C' and resid 27 through 1309) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.610 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 28365 Z= 0.208 Angle : 0.700 11.763 38717 Z= 0.387 Chirality : 0.047 0.205 4557 Planarity : 0.005 0.055 4889 Dihedral : 11.081 87.332 11049 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.29 % Rotamer: Outliers : 0.30 % Allowed : 1.76 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3395 helix: 0.39 (0.18), residues: 681 sheet: 0.49 (0.17), residues: 873 loop : -0.15 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1019 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.002 PHE C 329 TRP 0.011 0.001 TRP C1102 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00440 (28262) covalent geometry : angle 0.69350 (38451) SS BOND : bond 0.00415 ( 43) SS BOND : angle 1.28817 ( 86) hydrogen bonds : bond 0.11695 ( 1132) hydrogen bonds : angle 7.31369 ( 3138) link_BETA1-4 : bond 0.00195 ( 15) link_BETA1-4 : angle 1.05426 ( 45) link_NAG-ASN : bond 0.00228 ( 45) link_NAG-ASN : angle 1.48195 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 339 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8323 (t0) cc_final: 0.7575 (m-30) REVERT: A 55 PHE cc_start: 0.7860 (m-80) cc_final: 0.7653 (m-80) REVERT: A 275 PHE cc_start: 0.7507 (m-80) cc_final: 0.7029 (m-80) REVERT: A 427 ASP cc_start: 0.8207 (m-30) cc_final: 0.7918 (t0) REVERT: A 486 PHE cc_start: 0.8257 (t80) cc_final: 0.7861 (t80) REVERT: A 610 VAL cc_start: 0.9167 (t) cc_final: 0.8935 (p) REVERT: A 900 MET cc_start: 0.8561 (mtp) cc_final: 0.8165 (mtp) REVERT: A 1029 MET cc_start: 0.8588 (tpp) cc_final: 0.8385 (tpp) REVERT: B 409 GLN cc_start: 0.7492 (mt0) cc_final: 0.6607 (mt0) REVERT: B 960 ASN cc_start: 0.7512 (m-40) cc_final: 0.7222 (t0) REVERT: C 449 TYR cc_start: 0.8590 (m-80) cc_final: 0.7953 (m-10) REVERT: C 451 TYR cc_start: 0.6344 (m-80) cc_final: 0.5936 (m-80) REVERT: C 1037 SER cc_start: 0.8772 (t) cc_final: 0.8153 (p) REVERT: H 73 ASP cc_start: 0.9309 (t0) cc_final: 0.9087 (t0) REVERT: H 74 ASN cc_start: 0.7977 (m-40) cc_final: 0.7440 (m-40) REVERT: H 158 PHE cc_start: 0.9149 (t80) cc_final: 0.8938 (t80) REVERT: L 35 TRP cc_start: 0.6997 (m100) cc_final: 0.6551 (m100) REVERT: L 36 TYR cc_start: 0.7796 (m-80) cc_final: 0.7129 (m-80) REVERT: L 48 ILE cc_start: 0.8677 (mm) cc_final: 0.8351 (mt) REVERT: L 95 LEU cc_start: 0.9698 (mt) cc_final: 0.9398 (tp) outliers start: 9 outliers final: 3 residues processed: 348 average time/residue: 0.2022 time to fit residues: 107.9792 Evaluate side-chains 175 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 955 ASN A1002 GLN B 121 ASN B 955 ASN C 196 ASN H 39 GLN L 38 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.139020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088242 restraints weight = 70961.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091293 restraints weight = 32022.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093158 restraints weight = 20165.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094376 restraints weight = 15446.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.095109 restraints weight = 13200.026| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28365 Z= 0.121 Angle : 0.572 7.617 38717 Z= 0.303 Chirality : 0.045 0.198 4557 Planarity : 0.004 0.055 4889 Dihedral : 6.415 59.530 4944 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.73 % Allowed : 6.09 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.76 (0.14), residues: 3395 helix: 1.61 (0.20), residues: 690 sheet: 0.81 (0.16), residues: 897 loop : -0.02 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 72 TYR 0.026 0.001 TYR L 173 PHE 0.030 0.002 PHE H 104 TRP 0.022 0.001 TRP H 36 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00260 (28262) covalent geometry : angle 0.56444 (38451) SS BOND : bond 0.00394 ( 43) SS BOND : angle 1.08872 ( 86) hydrogen bonds : bond 0.04324 ( 1132) hydrogen bonds : angle 5.84502 ( 3138) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.03198 ( 45) link_NAG-ASN : bond 0.00272 ( 45) link_NAG-ASN : angle 1.44045 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9234 (t80) cc_final: 0.8565 (t80) REVERT: A 194 PHE cc_start: 0.8549 (m-80) cc_final: 0.8319 (m-10) REVERT: A 275 PHE cc_start: 0.7614 (m-80) cc_final: 0.7142 (m-80) REVERT: A 427 ASP cc_start: 0.8439 (m-30) cc_final: 0.7970 (t0) REVERT: A 486 PHE cc_start: 0.8570 (t80) cc_final: 0.8151 (t80) REVERT: A 508 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 610 VAL cc_start: 0.9136 (t) cc_final: 0.8936 (m) REVERT: A 731 MET cc_start: 0.7870 (ptm) cc_final: 0.7552 (ptm) REVERT: A 1029 MET cc_start: 0.8177 (tpp) cc_final: 0.7953 (tpp) REVERT: B 378 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8224 (mtmm) REVERT: B 427 ASP cc_start: 0.8918 (m-30) cc_final: 0.8708 (m-30) REVERT: B 462 LYS cc_start: 0.8774 (mttm) cc_final: 0.8411 (mttp) REVERT: B 516 GLU cc_start: 0.6663 (pt0) cc_final: 0.6406 (pt0) REVERT: B 582 LEU cc_start: 0.9043 (mm) cc_final: 0.8775 (mm) REVERT: B 869 MET cc_start: 0.8304 (mtt) cc_final: 0.7741 (mmm) REVERT: B 960 ASN cc_start: 0.7497 (m-40) cc_final: 0.6888 (t0) REVERT: C 56 LEU cc_start: 0.7175 (tp) cc_final: 0.6599 (tp) REVERT: C 86 PHE cc_start: 0.7345 (t80) cc_final: 0.7130 (t80) REVERT: C 118 LEU cc_start: 0.6725 (tp) cc_final: 0.6486 (mm) REVERT: C 238 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7362 (p90) REVERT: C 378 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6893 (mmtt) REVERT: C 449 TYR cc_start: 0.8765 (m-80) cc_final: 0.8188 (m-10) REVERT: C 902 MET cc_start: 0.8334 (mmm) cc_final: 0.7986 (mmt) REVERT: C 1037 SER cc_start: 0.8774 (t) cc_final: 0.8066 (p) REVERT: H 103 ARG cc_start: 0.9195 (mmm160) cc_final: 0.8974 (mmm160) REVERT: H 120 MET cc_start: 0.7996 (tpp) cc_final: 0.7784 (tpp) REVERT: L 36 TYR cc_start: 0.8738 (m-80) cc_final: 0.8420 (m-80) REVERT: L 48 ILE cc_start: 0.8594 (mm) cc_final: 0.8254 (mm) outliers start: 22 outliers final: 13 residues processed: 218 average time/residue: 0.1854 time to fit residues: 63.9111 Evaluate side-chains 152 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 134 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 224 optimal weight: 0.4980 chunk 180 optimal weight: 0.0470 chunk 281 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 272 optimal weight: 0.0770 chunk 279 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 314 optimal weight: 50.0000 chunk 198 optimal weight: 0.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 125 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.138411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090445 restraints weight = 71070.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092950 restraints weight = 39432.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094547 restraints weight = 23810.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094708 restraints weight = 23742.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094654 restraints weight = 18734.527| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28365 Z= 0.119 Angle : 0.522 10.566 38717 Z= 0.274 Chirality : 0.044 0.188 4557 Planarity : 0.004 0.045 4889 Dihedral : 5.680 59.525 4944 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 6.05 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.88 (0.14), residues: 3395 helix: 1.80 (0.20), residues: 688 sheet: 0.78 (0.16), residues: 915 loop : 0.07 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.015 0.001 TYR C1067 PHE 0.027 0.001 PHE A 823 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00265 (28262) covalent geometry : angle 0.51315 (38451) SS BOND : bond 0.00228 ( 43) SS BOND : angle 1.12688 ( 86) hydrogen bonds : bond 0.03900 ( 1132) hydrogen bonds : angle 5.46443 ( 3138) link_BETA1-4 : bond 0.00503 ( 15) link_BETA1-4 : angle 1.12226 ( 45) link_NAG-ASN : bond 0.00195 ( 45) link_NAG-ASN : angle 1.34017 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9273 (t80) cc_final: 0.8589 (t80) REVERT: A 427 ASP cc_start: 0.8370 (m-30) cc_final: 0.7957 (t0) REVERT: A 486 PHE cc_start: 0.8821 (t80) cc_final: 0.8393 (t80) REVERT: A 508 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6827 (t80) REVERT: A 731 MET cc_start: 0.7897 (ptm) cc_final: 0.7451 (ptm) REVERT: A 900 MET cc_start: 0.8511 (mtp) cc_final: 0.8175 (mtp) REVERT: A 1029 MET cc_start: 0.8084 (tpp) cc_final: 0.7869 (tpp) REVERT: B 378 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8392 (mtmm) REVERT: B 427 ASP cc_start: 0.8868 (m-30) cc_final: 0.8644 (m-30) REVERT: B 462 LYS cc_start: 0.8908 (mttm) cc_final: 0.8401 (ptmm) REVERT: B 516 GLU cc_start: 0.6709 (pt0) cc_final: 0.5655 (pm20) REVERT: B 869 MET cc_start: 0.8354 (mtt) cc_final: 0.7841 (mmm) REVERT: B 960 ASN cc_start: 0.7505 (m-40) cc_final: 0.6941 (t0) REVERT: B 1076 THR cc_start: 0.8713 (m) cc_final: 0.8189 (p) REVERT: C 86 PHE cc_start: 0.7562 (t80) cc_final: 0.7279 (t80) REVERT: C 104 TRP cc_start: 0.8615 (m-10) cc_final: 0.8241 (m-10) REVERT: C 238 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7541 (p90) REVERT: C 378 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6632 (mmtt) REVERT: C 410 ILE cc_start: 0.7936 (mm) cc_final: 0.7126 (mp) REVERT: C 449 TYR cc_start: 0.8799 (m-80) cc_final: 0.8237 (m-10) REVERT: C 513 LEU cc_start: 0.8976 (tp) cc_final: 0.8614 (tt) REVERT: C 902 MET cc_start: 0.8432 (mmm) cc_final: 0.8160 (mmt) REVERT: C 1037 SER cc_start: 0.8862 (t) cc_final: 0.8166 (p) REVERT: H 103 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8494 (mmm160) REVERT: H 104 PHE cc_start: 0.8370 (t80) cc_final: 0.8163 (t80) REVERT: H 115 TRP cc_start: 0.6783 (m-10) cc_final: 0.6413 (m-90) REVERT: H 158 PHE cc_start: 0.8735 (t80) cc_final: 0.8336 (t80) REVERT: L 36 TYR cc_start: 0.8224 (m-80) cc_final: 0.7909 (m-80) REVERT: L 92 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.7563 (m-40) outliers start: 33 outliers final: 21 residues processed: 173 average time/residue: 0.1781 time to fit residues: 49.8647 Evaluate side-chains 149 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 239 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 321 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 254 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.135701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083715 restraints weight = 70719.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086312 restraints weight = 34742.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087771 restraints weight = 22725.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089200 restraints weight = 18243.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089807 restraints weight = 15517.816| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 28365 Z= 0.177 Angle : 0.551 10.643 38717 Z= 0.287 Chirality : 0.044 0.170 4557 Planarity : 0.004 0.045 4889 Dihedral : 5.192 56.459 4944 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.40 % Allowed : 6.75 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3395 helix: 1.69 (0.20), residues: 683 sheet: 0.78 (0.16), residues: 904 loop : 0.03 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 98 TYR 0.022 0.001 TYR C1067 PHE 0.036 0.002 PHE A 275 TRP 0.015 0.001 TRP H 36 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (28262) covalent geometry : angle 0.53798 (38451) SS BOND : bond 0.00403 ( 43) SS BOND : angle 1.93038 ( 86) hydrogen bonds : bond 0.03994 ( 1132) hydrogen bonds : angle 5.40196 ( 3138) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.19657 ( 45) link_NAG-ASN : bond 0.00274 ( 45) link_NAG-ASN : angle 1.35997 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9417 (t80) cc_final: 0.8587 (t80) REVERT: A 427 ASP cc_start: 0.8490 (m-30) cc_final: 0.8037 (t0) REVERT: A 486 PHE cc_start: 0.8681 (t80) cc_final: 0.8244 (t80) REVERT: B 378 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8160 (mtmm) REVERT: B 408 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8386 (ttp80) REVERT: B 414 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7853 (tp-100) REVERT: B 462 LYS cc_start: 0.8899 (mttm) cc_final: 0.8301 (ptmm) REVERT: B 582 LEU cc_start: 0.9099 (mm) cc_final: 0.8872 (mm) REVERT: B 869 MET cc_start: 0.8395 (mtt) cc_final: 0.7829 (mmm) REVERT: B 960 ASN cc_start: 0.7491 (m-40) cc_final: 0.6888 (t0) REVERT: B 1076 THR cc_start: 0.8736 (m) cc_final: 0.8186 (p) REVERT: C 86 PHE cc_start: 0.7335 (t80) cc_final: 0.6804 (t80) REVERT: C 104 TRP cc_start: 0.8546 (m-10) cc_final: 0.8143 (m-10) REVERT: C 118 LEU cc_start: 0.7246 (tp) cc_final: 0.6410 (mm) REVERT: C 238 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7351 (p90) REVERT: C 378 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6644 (mmtt) REVERT: C 410 ILE cc_start: 0.8145 (mm) cc_final: 0.7541 (mp) REVERT: C 449 TYR cc_start: 0.8859 (m-80) cc_final: 0.8334 (m-10) REVERT: C 513 LEU cc_start: 0.9074 (tp) cc_final: 0.8780 (tt) REVERT: H 38 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7697 (ttt90) REVERT: H 103 ARG cc_start: 0.9102 (mmm160) cc_final: 0.8621 (mmm160) REVERT: H 104 PHE cc_start: 0.8847 (t80) cc_final: 0.8616 (t80) REVERT: L 92 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8499 (m-40) outliers start: 42 outliers final: 25 residues processed: 175 average time/residue: 0.1760 time to fit residues: 50.0384 Evaluate side-chains 151 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 291 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 268 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 913 GLN C1106 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.135113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083914 restraints weight = 70771.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088320 restraints weight = 35851.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088529 restraints weight = 22518.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089387 restraints weight = 17244.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.089602 restraints weight = 15900.378| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28365 Z= 0.175 Angle : 0.537 7.575 38717 Z= 0.278 Chirality : 0.044 0.207 4557 Planarity : 0.004 0.048 4889 Dihedral : 4.817 51.926 4944 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.40 % Allowed : 7.45 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.72 (0.14), residues: 3395 helix: 1.63 (0.20), residues: 690 sheet: 0.68 (0.16), residues: 927 loop : -0.02 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.022 0.001 TYR C1067 PHE 0.028 0.002 PHE A 275 TRP 0.015 0.001 TRP H 36 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00408 (28262) covalent geometry : angle 0.52910 (38451) SS BOND : bond 0.00250 ( 43) SS BOND : angle 1.18625 ( 86) hydrogen bonds : bond 0.03943 ( 1132) hydrogen bonds : angle 5.29645 ( 3138) link_BETA1-4 : bond 0.00200 ( 15) link_BETA1-4 : angle 1.19469 ( 45) link_NAG-ASN : bond 0.00271 ( 45) link_NAG-ASN : angle 1.31552 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9474 (t80) cc_final: 0.8560 (t80) REVERT: A 427 ASP cc_start: 0.8417 (m-30) cc_final: 0.7902 (t0) REVERT: A 486 PHE cc_start: 0.8947 (t80) cc_final: 0.8525 (t80) REVERT: A 900 MET cc_start: 0.8403 (mtt) cc_final: 0.8093 (mtp) REVERT: B 408 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8383 (ttp80) REVERT: B 414 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7880 (tp-100) REVERT: B 462 LYS cc_start: 0.8857 (mttm) cc_final: 0.8501 (ptmm) REVERT: B 869 MET cc_start: 0.8401 (mtt) cc_final: 0.8165 (tpp) REVERT: B 902 MET cc_start: 0.8668 (tpt) cc_final: 0.8396 (tpt) REVERT: B 960 ASN cc_start: 0.7457 (m-40) cc_final: 0.6832 (t0) REVERT: B 1076 THR cc_start: 0.8711 (m) cc_final: 0.8189 (p) REVERT: C 104 TRP cc_start: 0.8702 (m-10) cc_final: 0.8271 (m-10) REVERT: C 196 ASN cc_start: 0.5752 (OUTLIER) cc_final: 0.5369 (p0) REVERT: C 238 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7624 (p90) REVERT: C 242 LEU cc_start: 0.8710 (mm) cc_final: 0.8434 (mm) REVERT: C 378 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6775 (mmtt) REVERT: C 410 ILE cc_start: 0.8170 (mm) cc_final: 0.7591 (mp) REVERT: C 449 TYR cc_start: 0.8956 (m-80) cc_final: 0.8503 (m-10) REVERT: C 508 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: C 759 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7244 (t80) REVERT: H 38 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7818 (ttt90) REVERT: H 103 ARG cc_start: 0.9275 (mmm160) cc_final: 0.8798 (mmm160) REVERT: L 29 ILE cc_start: 0.6516 (mp) cc_final: 0.5983 (mp) outliers start: 42 outliers final: 28 residues processed: 171 average time/residue: 0.1631 time to fit residues: 45.4986 Evaluate side-chains 152 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 139 optimal weight: 0.7980 chunk 285 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 613 GLN A 957 GLN B1135 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.135666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083446 restraints weight = 70638.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086337 restraints weight = 33773.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088023 restraints weight = 21712.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089126 restraints weight = 16850.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.089862 restraints weight = 14603.347| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28365 Z= 0.122 Angle : 0.499 10.380 38717 Z= 0.258 Chirality : 0.043 0.160 4557 Planarity : 0.003 0.045 4889 Dihedral : 4.502 51.845 4944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 8.15 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.78 (0.14), residues: 3395 helix: 1.78 (0.21), residues: 692 sheet: 0.61 (0.16), residues: 917 loop : 0.05 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.020 0.001 TYR C 369 PHE 0.022 0.001 PHE H 104 TRP 0.026 0.001 TRP H 115 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00281 (28262) covalent geometry : angle 0.49176 (38451) SS BOND : bond 0.00236 ( 43) SS BOND : angle 0.90001 ( 86) hydrogen bonds : bond 0.03656 ( 1132) hydrogen bonds : angle 5.16110 ( 3138) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.17575 ( 45) link_NAG-ASN : bond 0.00210 ( 45) link_NAG-ASN : angle 1.21360 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9328 (t80) cc_final: 0.8476 (t80) REVERT: A 427 ASP cc_start: 0.8427 (m-30) cc_final: 0.7906 (t0) REVERT: A 486 PHE cc_start: 0.8695 (t80) cc_final: 0.8250 (t80) REVERT: A 900 MET cc_start: 0.8347 (mtt) cc_final: 0.8053 (mtp) REVERT: B 392 PHE cc_start: 0.7223 (m-80) cc_final: 0.6535 (m-80) REVERT: B 408 ARG cc_start: 0.8776 (ttp80) cc_final: 0.7904 (tmm160) REVERT: B 414 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7888 (tm-30) REVERT: B 462 LYS cc_start: 0.8710 (mttm) cc_final: 0.8411 (ptmm) REVERT: B 869 MET cc_start: 0.8381 (mtt) cc_final: 0.8163 (tpp) REVERT: B 960 ASN cc_start: 0.7377 (m-40) cc_final: 0.6940 (t0) REVERT: B 1076 THR cc_start: 0.8756 (m) cc_final: 0.8207 (p) REVERT: C 104 TRP cc_start: 0.8359 (m-10) cc_final: 0.7910 (m-10) REVERT: C 238 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7233 (p90) REVERT: C 242 LEU cc_start: 0.8505 (mm) cc_final: 0.8232 (mm) REVERT: C 378 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6882 (mmtt) REVERT: C 410 ILE cc_start: 0.8154 (mm) cc_final: 0.7788 (mp) REVERT: C 436 TRP cc_start: 0.9011 (p90) cc_final: 0.8384 (p90) REVERT: C 449 TYR cc_start: 0.8886 (m-80) cc_final: 0.8390 (m-10) REVERT: C 508 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: C 753 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7672 (tp) REVERT: C 759 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7232 (t80) REVERT: H 38 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8116 (ttt90) outliers start: 38 outliers final: 23 residues processed: 163 average time/residue: 0.1711 time to fit residues: 45.6403 Evaluate side-chains 149 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 163 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 339 optimal weight: 50.0000 chunk 258 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 131 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN A1088 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081577 restraints weight = 70456.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084168 restraints weight = 33872.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086075 restraints weight = 22288.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087077 restraints weight = 17452.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087967 restraints weight = 15166.447| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 28365 Z= 0.177 Angle : 0.552 12.042 38717 Z= 0.284 Chirality : 0.044 0.171 4557 Planarity : 0.004 0.044 4889 Dihedral : 4.448 52.145 4943 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.20 % Allowed : 8.55 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.71 (0.14), residues: 3395 helix: 1.65 (0.21), residues: 683 sheet: 0.63 (0.17), residues: 913 loop : -0.00 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.023 0.001 TYR C1067 PHE 0.023 0.001 PHE A 275 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00418 (28262) covalent geometry : angle 0.53322 (38451) SS BOND : bond 0.00301 ( 43) SS BOND : angle 2.54726 ( 86) hydrogen bonds : bond 0.03865 ( 1132) hydrogen bonds : angle 5.27016 ( 3138) link_BETA1-4 : bond 0.00257 ( 15) link_BETA1-4 : angle 1.22540 ( 45) link_NAG-ASN : bond 0.00274 ( 45) link_NAG-ASN : angle 1.27616 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9357 (t80) cc_final: 0.8507 (t80) REVERT: A 414 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7962 (mm-40) REVERT: A 427 ASP cc_start: 0.8421 (m-30) cc_final: 0.7917 (t0) REVERT: A 486 PHE cc_start: 0.8708 (t80) cc_final: 0.8253 (t80) REVERT: A 755 GLN cc_start: 0.7938 (mt0) cc_final: 0.7596 (mt0) REVERT: A 869 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7813 (ttm) REVERT: A 900 MET cc_start: 0.8402 (mtt) cc_final: 0.8133 (mtp) REVERT: A 957 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: B 392 PHE cc_start: 0.7423 (m-80) cc_final: 0.6842 (m-80) REVERT: B 408 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8344 (tmm160) REVERT: B 414 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8001 (tp40) REVERT: B 462 LYS cc_start: 0.8740 (mttm) cc_final: 0.8405 (ptmm) REVERT: B 869 MET cc_start: 0.8429 (mtt) cc_final: 0.7924 (mmm) REVERT: B 960 ASN cc_start: 0.7378 (m-40) cc_final: 0.7133 (t0) REVERT: B 1076 THR cc_start: 0.8618 (m) cc_final: 0.8121 (p) REVERT: C 104 TRP cc_start: 0.8403 (m-10) cc_final: 0.7942 (m-10) REVERT: C 238 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7225 (p90) REVERT: C 242 LEU cc_start: 0.8522 (mm) cc_final: 0.8253 (mm) REVERT: C 410 ILE cc_start: 0.8178 (mm) cc_final: 0.7769 (mp) REVERT: C 436 TRP cc_start: 0.9036 (p90) cc_final: 0.8400 (p90) REVERT: C 449 TYR cc_start: 0.8885 (m-80) cc_final: 0.8432 (m-10) REVERT: C 508 TYR cc_start: 0.9273 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: H 34 MET cc_start: 0.9696 (mmp) cc_final: 0.7841 (tmm) REVERT: H 103 ARG cc_start: 0.9290 (mmm160) cc_final: 0.8946 (mmm160) outliers start: 36 outliers final: 29 residues processed: 167 average time/residue: 0.1699 time to fit residues: 46.4086 Evaluate side-chains 156 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 249 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 152 optimal weight: 0.4980 chunk 100 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 333 optimal weight: 50.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN C 125 ASN C 196 ASN C 450 ASN H 39 GLN L 38 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080397 restraints weight = 70705.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083383 restraints weight = 34306.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085154 restraints weight = 22449.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086392 restraints weight = 17762.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.087044 restraints weight = 15370.080| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28365 Z= 0.199 Angle : 0.562 11.429 38717 Z= 0.290 Chirality : 0.044 0.161 4557 Planarity : 0.004 0.044 4889 Dihedral : 4.433 51.894 4943 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.23 % Allowed : 9.05 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.61 (0.14), residues: 3395 helix: 1.63 (0.20), residues: 677 sheet: 0.52 (0.17), residues: 906 loop : -0.05 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 38 TYR 0.025 0.001 TYR C1067 PHE 0.040 0.002 PHE A 275 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00469 (28262) covalent geometry : angle 0.54685 (38451) SS BOND : bond 0.00280 ( 43) SS BOND : angle 2.23829 ( 86) hydrogen bonds : bond 0.03988 ( 1132) hydrogen bonds : angle 5.30811 ( 3138) link_BETA1-4 : bond 0.00272 ( 15) link_BETA1-4 : angle 1.24048 ( 45) link_NAG-ASN : bond 0.00302 ( 45) link_NAG-ASN : angle 1.29588 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9358 (t80) cc_final: 0.8524 (t80) REVERT: A 383 SER cc_start: 0.8484 (m) cc_final: 0.8023 (t) REVERT: A 414 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8005 (mm-40) REVERT: A 427 ASP cc_start: 0.8412 (m-30) cc_final: 0.7916 (t0) REVERT: A 486 PHE cc_start: 0.8681 (t80) cc_final: 0.8228 (t80) REVERT: A 755 GLN cc_start: 0.8095 (mt0) cc_final: 0.7789 (mt0) REVERT: A 869 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7826 (ttm) REVERT: A 900 MET cc_start: 0.8425 (mtt) cc_final: 0.8162 (mtp) REVERT: B 392 PHE cc_start: 0.7585 (m-80) cc_final: 0.7006 (m-80) REVERT: B 408 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8232 (tmm160) REVERT: B 414 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7777 (tp40) REVERT: B 462 LYS cc_start: 0.8765 (mttm) cc_final: 0.8428 (ptmm) REVERT: B 869 MET cc_start: 0.8444 (mtt) cc_final: 0.7970 (mmm) REVERT: B 960 ASN cc_start: 0.7419 (m-40) cc_final: 0.7156 (t0) REVERT: B 1076 THR cc_start: 0.8653 (m) cc_final: 0.8156 (p) REVERT: C 104 TRP cc_start: 0.8331 (m-10) cc_final: 0.7804 (m-10) REVERT: C 238 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7219 (p90) REVERT: C 242 LEU cc_start: 0.8530 (mm) cc_final: 0.8267 (mm) REVERT: C 378 LYS cc_start: 0.7461 (mmmt) cc_final: 0.6973 (mmtt) REVERT: C 436 TRP cc_start: 0.8977 (p90) cc_final: 0.8292 (p90) REVERT: C 449 TYR cc_start: 0.8862 (m-80) cc_final: 0.8405 (m-10) REVERT: C 508 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: H 34 MET cc_start: 0.9683 (mmp) cc_final: 0.7714 (tmm) REVERT: H 103 ARG cc_start: 0.9313 (mmm160) cc_final: 0.8938 (mmm160) REVERT: L 36 TYR cc_start: 0.9702 (OUTLIER) cc_final: 0.9204 (t80) outliers start: 37 outliers final: 29 residues processed: 156 average time/residue: 0.1684 time to fit residues: 42.3942 Evaluate side-chains 155 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 15 optimal weight: 0.6980 chunk 326 optimal weight: 6.9990 chunk 338 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 96 optimal weight: 0.8980 chunk 211 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080894 restraints weight = 70429.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083448 restraints weight = 34036.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085179 restraints weight = 22611.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086359 restraints weight = 17684.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086951 restraints weight = 15324.128| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28365 Z= 0.180 Angle : 0.550 10.194 38717 Z= 0.282 Chirality : 0.044 0.161 4557 Planarity : 0.004 0.044 4889 Dihedral : 4.382 51.815 4943 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.23 % Allowed : 9.05 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.58 (0.14), residues: 3395 helix: 1.67 (0.21), residues: 677 sheet: 0.40 (0.16), residues: 954 loop : -0.05 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.023 0.001 TYR C1067 PHE 0.032 0.001 PHE A 275 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00423 (28262) covalent geometry : angle 0.53818 (38451) SS BOND : bond 0.00267 ( 43) SS BOND : angle 1.85349 ( 86) hydrogen bonds : bond 0.03872 ( 1132) hydrogen bonds : angle 5.25992 ( 3138) link_BETA1-4 : bond 0.00247 ( 15) link_BETA1-4 : angle 1.20331 ( 45) link_NAG-ASN : bond 0.00268 ( 45) link_NAG-ASN : angle 1.24253 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9354 (t80) cc_final: 0.8549 (t80) REVERT: A 383 SER cc_start: 0.8521 (m) cc_final: 0.8062 (t) REVERT: A 414 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7877 (mm-40) REVERT: A 427 ASP cc_start: 0.8400 (m-30) cc_final: 0.7901 (t0) REVERT: A 486 PHE cc_start: 0.8762 (t80) cc_final: 0.8308 (t80) REVERT: A 755 GLN cc_start: 0.8087 (mt0) cc_final: 0.7812 (mt0) REVERT: A 869 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7800 (ttm) REVERT: A 900 MET cc_start: 0.8419 (mtt) cc_final: 0.8147 (mtp) REVERT: A 904 TYR cc_start: 0.6872 (m-10) cc_final: 0.6546 (m-10) REVERT: B 88 ASP cc_start: 0.8674 (p0) cc_final: 0.7520 (t0) REVERT: B 392 PHE cc_start: 0.7633 (m-80) cc_final: 0.7086 (m-80) REVERT: B 462 LYS cc_start: 0.8830 (mttm) cc_final: 0.8543 (ptmm) REVERT: B 869 MET cc_start: 0.8428 (mtt) cc_final: 0.7983 (mmm) REVERT: B 960 ASN cc_start: 0.7390 (m-40) cc_final: 0.7155 (t0) REVERT: B 1076 THR cc_start: 0.8650 (m) cc_final: 0.8153 (p) REVERT: C 104 TRP cc_start: 0.8350 (m-10) cc_final: 0.7808 (m-10) REVERT: C 238 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7198 (p90) REVERT: C 242 LEU cc_start: 0.8576 (mm) cc_final: 0.8337 (mm) REVERT: C 378 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6822 (mmtt) REVERT: C 408 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8882 (ttp80) REVERT: C 436 TRP cc_start: 0.8939 (p90) cc_final: 0.8233 (p90) REVERT: C 449 TYR cc_start: 0.8839 (m-80) cc_final: 0.8382 (m-10) REVERT: C 508 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: H 34 MET cc_start: 0.9584 (mmp) cc_final: 0.7502 (mmm) REVERT: H 103 ARG cc_start: 0.9390 (mmm160) cc_final: 0.9034 (mmm160) REVERT: L 35 TRP cc_start: 0.6793 (m100) cc_final: 0.5251 (m100) REVERT: L 36 TYR cc_start: 0.9698 (OUTLIER) cc_final: 0.9189 (t80) outliers start: 37 outliers final: 29 residues processed: 158 average time/residue: 0.1811 time to fit residues: 46.8191 Evaluate side-chains 159 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 98 optimal weight: 0.8980 chunk 321 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 296 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.134592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081615 restraints weight = 69984.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084657 restraints weight = 33665.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086433 restraints weight = 21947.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.087195 restraints weight = 17098.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088129 restraints weight = 15211.341| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28365 Z= 0.132 Angle : 0.524 11.163 38717 Z= 0.269 Chirality : 0.044 0.155 4557 Planarity : 0.004 0.043 4889 Dihedral : 4.244 51.755 4943 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.06 % Allowed : 9.28 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.63 (0.15), residues: 3395 helix: 1.91 (0.21), residues: 663 sheet: 0.35 (0.16), residues: 982 loop : -0.05 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE A 275 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00307 (28262) covalent geometry : angle 0.51332 (38451) SS BOND : bond 0.00245 ( 43) SS BOND : angle 1.76987 ( 86) hydrogen bonds : bond 0.03685 ( 1132) hydrogen bonds : angle 5.15079 ( 3138) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 1.15801 ( 45) link_NAG-ASN : bond 0.00206 ( 45) link_NAG-ASN : angle 1.17323 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9365 (t80) cc_final: 0.8557 (t80) REVERT: A 383 SER cc_start: 0.8647 (m) cc_final: 0.7995 (t) REVERT: A 427 ASP cc_start: 0.8405 (m-30) cc_final: 0.7892 (t0) REVERT: A 486 PHE cc_start: 0.8718 (t80) cc_final: 0.8262 (t80) REVERT: A 492 LEU cc_start: 0.8916 (mp) cc_final: 0.8421 (tp) REVERT: A 755 GLN cc_start: 0.8124 (mt0) cc_final: 0.7795 (mt0) REVERT: A 900 MET cc_start: 0.8374 (mtt) cc_final: 0.8023 (mtp) REVERT: A 904 TYR cc_start: 0.6843 (m-10) cc_final: 0.6495 (m-10) REVERT: B 88 ASP cc_start: 0.8646 (p0) cc_final: 0.7480 (t0) REVERT: B 392 PHE cc_start: 0.7588 (m-80) cc_final: 0.7046 (m-80) REVERT: B 462 LYS cc_start: 0.8840 (mttm) cc_final: 0.8536 (ptmm) REVERT: B 960 ASN cc_start: 0.7348 (m-40) cc_final: 0.7136 (t0) REVERT: B 1076 THR cc_start: 0.8477 (m) cc_final: 0.7925 (p) REVERT: C 104 TRP cc_start: 0.8402 (m-10) cc_final: 0.7803 (m-10) REVERT: C 238 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7167 (p90) REVERT: C 242 LEU cc_start: 0.8581 (mm) cc_final: 0.8348 (mm) REVERT: C 378 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7238 (mmtt) REVERT: C 415 THR cc_start: 0.8558 (p) cc_final: 0.8291 (m) REVERT: C 436 TRP cc_start: 0.8938 (p90) cc_final: 0.8206 (p90) REVERT: C 449 TYR cc_start: 0.8852 (m-80) cc_final: 0.8399 (m-10) REVERT: C 508 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: H 34 MET cc_start: 0.9528 (mmp) cc_final: 0.7510 (mmm) REVERT: H 67 ARG cc_start: 0.6900 (ptm160) cc_final: 0.6586 (ptm160) REVERT: H 68 PHE cc_start: 0.8127 (m-80) cc_final: 0.7434 (m-80) REVERT: H 103 ARG cc_start: 0.9433 (mmm160) cc_final: 0.9078 (mmm160) REVERT: L 35 TRP cc_start: 0.6897 (m100) cc_final: 0.5430 (m100) REVERT: L 36 TYR cc_start: 0.9695 (OUTLIER) cc_final: 0.9146 (t80) outliers start: 32 outliers final: 27 residues processed: 156 average time/residue: 0.1777 time to fit residues: 45.1289 Evaluate side-chains 155 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 152 optimal weight: 0.0870 chunk 325 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 327 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.133131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079858 restraints weight = 70504.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082547 restraints weight = 34314.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084343 restraints weight = 22602.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085354 restraints weight = 17910.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.085946 restraints weight = 15568.063| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28365 Z= 0.227 Angle : 0.594 10.393 38717 Z= 0.304 Chirality : 0.045 0.180 4557 Planarity : 0.004 0.040 4889 Dihedral : 4.511 51.939 4943 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.06 % Allowed : 9.35 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.46 (0.15), residues: 3395 helix: 1.62 (0.21), residues: 657 sheet: 0.32 (0.16), residues: 951 loop : -0.13 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 408 TYR 0.024 0.001 TYR C1067 PHE 0.027 0.002 PHE A 275 TRP 0.012 0.001 TRP C 436 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00533 (28262) covalent geometry : angle 0.58173 (38451) SS BOND : bond 0.00333 ( 43) SS BOND : angle 1.95552 ( 86) hydrogen bonds : bond 0.04182 ( 1132) hydrogen bonds : angle 5.35853 ( 3138) link_BETA1-4 : bond 0.00219 ( 15) link_BETA1-4 : angle 1.27187 ( 45) link_NAG-ASN : bond 0.00359 ( 45) link_NAG-ASN : angle 1.34692 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6273.51 seconds wall clock time: 108 minutes 15.53 seconds (6495.53 seconds total)