Starting phenix.real_space_refine on Mon Aug 25 14:37:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g75_29797/08_2025/8g75_29797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g75_29797/08_2025/8g75_29797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g75_29797/08_2025/8g75_29797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g75_29797/08_2025/8g75_29797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g75_29797/08_2025/8g75_29797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g75_29797/08_2025/8g75_29797.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18226 2.51 5 N 4748 2.21 5 O 5608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28711 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.02, per 1000 atoms: 0.28 Number of scatterers: 28711 At special positions: 0 Unit cell: (156.704, 164.672, 196.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5608 8.00 N 4748 7.00 C 18226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.04 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=2.03 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 D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1074 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 616 " " NAG D1304 " - " ASN D 657 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN D 717 " " NAG O 1 " - " ASN D 801 " " NAG P 1 " - " ASN D1098 " " NAG Q 1 " - " ASN D1134 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.165A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.810A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.824A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.569A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.940A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.578A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.507A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.540A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.595A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.501A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.871A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.807A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (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 337 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.032A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.704A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.787A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.315A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.742A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.649A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.748A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.546A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.778A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.614A pdb=" N LYS D 386 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 387' Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.783A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.600A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.749A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.339A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.701A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.441A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1147 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.922A pdb=" N TYR E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.717A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.952A pdb=" N TYR F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR F 32 " --> pdb=" O LEU F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.216A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.576A 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: 3.738A pdb=" N ARG D 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.780A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.782A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.662A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.852A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.405A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.164A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) 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 565 through 566 removed outlier: 6.573A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.512A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.552A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.647A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.367A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.350A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.765A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.682A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.773A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.975A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.883A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.635A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.652A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.653A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 7.990A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.741A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.588A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 removed outlier: 12.725A pdb=" N PHE D 135 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 12.622A pdb=" N THR D 240 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N ASN D 137 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N LEU D 242 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 140 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.594A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.206A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 593 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.680A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.644A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 removed outlier: 4.145A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.625A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.330A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.296A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG E 38 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.737A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG G 38 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.562A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 38 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 12 1153 hydrogen bonds defined for protein. 3090 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: 8.37 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8742 1.34 - 1.46: 7711 1.46 - 1.59: 12759 1.59 - 1.72: 0 1.72 - 1.85: 162 Bond restraints: 29374 Sorted by residual: bond pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 1.00e+01 bond pdb=" C1 NAG D1303 " pdb=" O5 NAG D1303 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.14e+00 bond pdb=" N LYS B 811 " pdb=" CA LYS B 811 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 8.75e+00 bond pdb=" N VAL B1104 " pdb=" CA VAL B1104 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.10e+00 ... (remaining 29369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 39192 2.28 - 4.55: 703 4.55 - 6.83: 58 6.83 - 9.11: 17 9.11 - 11.39: 6 Bond angle restraints: 39976 Sorted by residual: angle pdb=" CA PRO B1143 " pdb=" N PRO B1143 " pdb=" CD PRO B1143 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA TRP D 436 " pdb=" CB TRP D 436 " pdb=" CG TRP D 436 " ideal model delta sigma weight residual 113.60 122.91 -9.31 1.90e+00 2.77e-01 2.40e+01 angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 123.35 -8.95 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N GLY A 485 " pdb=" CA GLY A 485 " pdb=" C GLY A 485 " ideal model delta sigma weight residual 113.18 122.26 -9.08 2.37e+00 1.78e-01 1.47e+01 angle pdb=" C TRP E 104 " pdb=" N TYR E 105 " pdb=" CA TYR E 105 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 ... (remaining 39971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15958 17.94 - 35.89: 1582 35.89 - 53.83: 431 53.83 - 71.77: 66 71.77 - 89.72: 33 Dihedral angle restraints: 18070 sinusoidal: 7636 harmonic: 10434 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 7.59 85.41 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 170.19 -77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.99 76.99 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 18067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4537 0.126 - 0.251: 71 0.251 - 0.377: 9 0.377 - 0.503: 0 0.503 - 0.628: 2 Chirality restraints: 4619 Sorted by residual: chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 282 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" C1 NAG D1303 " pdb=" ND2 ASN D 616 " pdb=" C2 NAG D1303 " pdb=" O5 NAG D1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 4616 not shown) Planarity restraints: 5169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.062 2.00e-02 2.50e+03 5.11e-02 3.27e+01 pdb=" C7 NAG A1309 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1142 " 0.060 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B1143 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B1143 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1143 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 400 " 0.030 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE D 400 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 400 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 400 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 400 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 400 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 400 " 0.008 2.00e-02 2.50e+03 ... (remaining 5166 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 230 2.59 - 3.17: 23753 3.17 - 3.75: 43519 3.75 - 4.32: 60537 4.32 - 4.90: 99210 Nonbonded interactions: 227249 Sorted by model distance: nonbonded pdb=" NZ LYS A 417 " pdb=" OH TYR A 495 " model vdw 2.017 3.120 nonbonded pdb=" OG1 THR D 323 " pdb=" OE1 GLU D 324 " model vdw 2.102 3.040 nonbonded pdb=" O SER G 52 " pdb=" NH2 ARG G 72 " model vdw 2.105 3.120 nonbonded pdb=" OD1 ASN B 616 " pdb=" N CYS B 617 " model vdw 2.110 3.120 nonbonded pdb=" OH TYR B 37 " pdb=" OD1 ASP B 53 " model vdw 2.116 3.040 ... (remaining 227244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1306) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1306)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1306)) } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.180 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 0.062 29463 Z= 0.206 Angle : 0.752 20.858 40201 Z= 0.377 Chirality : 0.050 0.628 4619 Planarity : 0.006 0.096 5133 Dihedral : 15.318 89.718 11252 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 0.61 % Allowed : 19.09 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.13), residues: 3562 helix: 0.95 (0.20), residues: 687 sheet: 0.47 (0.17), residues: 811 loop : -0.87 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 454 TYR 0.049 0.002 TYR A 453 PHE 0.058 0.002 PHE D 400 TRP 0.033 0.002 TRP F 104 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00408 (29374) covalent geometry : angle 0.69735 (39976) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.39840 ( 84) hydrogen bonds : bond 0.23665 ( 1129) hydrogen bonds : angle 8.52813 ( 3090) link_BETA1-4 : bond 0.00378 ( 11) link_BETA1-4 : angle 1.58501 ( 33) link_NAG-ASN : bond 0.00859 ( 36) link_NAG-ASN : angle 5.33529 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 1.062 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 428 ASP cc_start: 0.6198 (p0) cc_final: 0.5973 (p0) REVERT: A 821 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8273 (tm) REVERT: B 900 MET cc_start: 0.8477 (ttm) cc_final: 0.8255 (mtm) REVERT: D 153 MET cc_start: 0.0085 (ptp) cc_final: -0.1163 (pmm) REVERT: D 602 THR cc_start: 0.7495 (p) cc_final: 0.7288 (p) outliers start: 19 outliers final: 8 residues processed: 233 average time/residue: 0.1782 time to fit residues: 70.0071 Evaluate side-chains 208 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 856 ASN A 926 GLN A 935 GLN A1010 GLN B 121 ASN B 804 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.229061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183167 restraints weight = 45574.455| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 3.86 r_work: 0.3766 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29463 Z= 0.185 Angle : 0.723 21.778 40201 Z= 0.364 Chirality : 0.049 0.532 4619 Planarity : 0.005 0.088 5133 Dihedral : 6.246 58.784 4874 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 2.69 % Allowed : 16.79 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.13), residues: 3562 helix: 1.58 (0.20), residues: 669 sheet: 0.38 (0.17), residues: 833 loop : -1.12 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 454 TYR 0.028 0.002 TYR A 351 PHE 0.031 0.002 PHE A 400 TRP 0.027 0.002 TRP D 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00422 (29374) covalent geometry : angle 0.68400 (39976) SS BOND : bond 0.00527 ( 42) SS BOND : angle 1.54611 ( 84) hydrogen bonds : bond 0.04977 ( 1129) hydrogen bonds : angle 5.99191 ( 3090) link_BETA1-4 : bond 0.00372 ( 11) link_BETA1-4 : angle 1.18574 ( 33) link_NAG-ASN : bond 0.00869 ( 36) link_NAG-ASN : angle 4.40020 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 221 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1418 (OUTLIER) cc_final: -0.0323 (mmm) REVERT: A 156 GLU cc_start: 0.3803 (tm-30) cc_final: 0.3570 (pp20) REVERT: A 157 PHE cc_start: 0.5614 (p90) cc_final: 0.5363 (m-10) REVERT: B 153 MET cc_start: 0.3232 (tpt) cc_final: 0.0150 (ptp) REVERT: B 160 TYR cc_start: 0.7182 (p90) cc_final: 0.6751 (p90) REVERT: B 1081 ILE cc_start: 0.8501 (mt) cc_final: 0.8212 (mt) REVERT: D 153 MET cc_start: -0.0047 (ptp) cc_final: -0.1344 (pmm) REVERT: D 950 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8049 (t0) REVERT: D 954 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7978 (mt0) REVERT: D 967 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8758 (m) REVERT: D 985 ASP cc_start: 0.6687 (t0) cc_final: 0.6382 (m-30) REVERT: E 125 VAL cc_start: 0.1518 (OUTLIER) cc_final: 0.1191 (t) outliers start: 84 outliers final: 31 residues processed: 290 average time/residue: 0.1671 time to fit residues: 83.1804 Evaluate side-chains 220 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 329 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 300 optimal weight: 0.1980 chunk 43 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 309 optimal weight: 0.2980 chunk 35 optimal weight: 8.9990 chunk 326 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 907 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN F 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.229008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.182697 restraints weight = 45048.709| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.79 r_work: 0.3771 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29463 Z= 0.121 Angle : 0.602 20.917 40201 Z= 0.302 Chirality : 0.045 0.485 4619 Planarity : 0.005 0.055 5133 Dihedral : 5.319 59.492 4863 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.02 % Rotamer: Outliers : 2.01 % Allowed : 17.65 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.14), residues: 3562 helix: 1.96 (0.20), residues: 700 sheet: 0.33 (0.17), residues: 831 loop : -1.02 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 103 TYR 0.027 0.001 TYR A 351 PHE 0.051 0.002 PHE D 400 TRP 0.024 0.001 TRP D 436 HIS 0.005 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00266 (29374) covalent geometry : angle 0.56664 (39976) SS BOND : bond 0.00420 ( 42) SS BOND : angle 1.05185 ( 84) hydrogen bonds : bond 0.04683 ( 1129) hydrogen bonds : angle 5.68822 ( 3090) link_BETA1-4 : bond 0.00371 ( 11) link_BETA1-4 : angle 1.22504 ( 33) link_NAG-ASN : bond 0.00691 ( 36) link_NAG-ASN : angle 3.82934 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.5902 (t80) cc_final: 0.4622 (t80) REVERT: B 153 MET cc_start: 0.2956 (tpt) cc_final: -0.0188 (ptp) REVERT: B 160 TYR cc_start: 0.7016 (p90) cc_final: 0.6783 (p90) REVERT: B 269 TYR cc_start: 0.7743 (m-10) cc_final: 0.7178 (m-80) REVERT: B 1081 ILE cc_start: 0.8460 (mt) cc_final: 0.8198 (mt) REVERT: D 153 MET cc_start: -0.0401 (ptp) cc_final: -0.1575 (pmm) REVERT: D 565 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: D 985 ASP cc_start: 0.6919 (t0) cc_final: 0.6620 (m-30) REVERT: D 1135 ASN cc_start: 0.6788 (t0) cc_final: 0.6581 (t0) outliers start: 63 outliers final: 30 residues processed: 267 average time/residue: 0.1791 time to fit residues: 80.4808 Evaluate side-chains 216 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 277 optimal weight: 0.4980 chunk 315 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 339 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 907 ASN B 957 GLN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN ** D1088 HIS ** 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 = 0.4651 r_free = 0.4651 target = 0.218555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.172160 restraints weight = 43436.657| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 3.79 r_work: 0.3678 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29463 Z= 0.150 Angle : 0.620 20.845 40201 Z= 0.311 Chirality : 0.046 0.466 4619 Planarity : 0.005 0.052 5133 Dihedral : 5.120 55.471 4862 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 3.13 % Allowed : 17.05 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.14), residues: 3562 helix: 2.02 (0.20), residues: 694 sheet: 0.41 (0.17), residues: 804 loop : -1.01 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 246 TYR 0.018 0.001 TYR A 351 PHE 0.043 0.002 PHE D 400 TRP 0.036 0.001 TRP D 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00345 (29374) covalent geometry : angle 0.58602 (39976) SS BOND : bond 0.00390 ( 42) SS BOND : angle 1.39814 ( 84) hydrogen bonds : bond 0.04634 ( 1129) hydrogen bonds : angle 5.45220 ( 3090) link_BETA1-4 : bond 0.00282 ( 11) link_BETA1-4 : angle 1.22687 ( 33) link_NAG-ASN : bond 0.00719 ( 36) link_NAG-ASN : angle 3.72245 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1996 (OUTLIER) cc_final: 0.1273 (mmm) REVERT: A 157 PHE cc_start: 0.6129 (m-10) cc_final: 0.5919 (m-10) REVERT: A 338 PHE cc_start: 0.6935 (m-80) cc_final: 0.6692 (m-80) REVERT: A 484 GLU cc_start: 0.3400 (OUTLIER) cc_final: 0.2717 (tp30) REVERT: A 753 LEU cc_start: 0.7519 (tp) cc_final: 0.7158 (tp) REVERT: A 983 ARG cc_start: 0.6354 (tpt90) cc_final: 0.6095 (ttt180) REVERT: B 153 MET cc_start: 0.2872 (tpt) cc_final: 0.2598 (tpt) REVERT: B 160 TYR cc_start: 0.6888 (p90) cc_final: 0.6559 (p90) REVERT: B 978 ASN cc_start: 0.7949 (m-40) cc_final: 0.7593 (m-40) REVERT: D 153 MET cc_start: -0.0403 (ptp) cc_final: -0.1507 (pmm) REVERT: D 565 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: D 823 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: D 984 LEU cc_start: 0.7617 (mm) cc_final: 0.7406 (mp) REVERT: D 985 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: D 1135 ASN cc_start: 0.7249 (t0) cc_final: 0.7037 (t0) outliers start: 98 outliers final: 58 residues processed: 270 average time/residue: 0.1726 time to fit residues: 78.8251 Evaluate side-chains 232 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 128 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 245 optimal weight: 0.2980 chunk 153 optimal weight: 20.0000 chunk 277 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 320 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 437 ASN ** D1088 HIS ** 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 = 0.4593 r_free = 0.4593 target = 0.212867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167444 restraints weight = 42795.233| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.80 r_work: 0.3599 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29463 Z= 0.153 Angle : 0.619 20.648 40201 Z= 0.311 Chirality : 0.046 0.439 4619 Planarity : 0.005 0.052 5133 Dihedral : 5.109 58.110 4862 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 2.85 % Allowed : 17.72 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.14), residues: 3562 helix: 2.01 (0.21), residues: 696 sheet: 0.42 (0.17), residues: 812 loop : -1.00 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 454 TYR 0.026 0.001 TYR D1138 PHE 0.025 0.002 PHE D 400 TRP 0.031 0.002 TRP D 436 HIS 0.005 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00358 (29374) covalent geometry : angle 0.58921 (39976) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.25909 ( 84) hydrogen bonds : bond 0.04889 ( 1129) hydrogen bonds : angle 5.36131 ( 3090) link_BETA1-4 : bond 0.00286 ( 11) link_BETA1-4 : angle 1.16875 ( 33) link_NAG-ASN : bond 0.00700 ( 36) link_NAG-ASN : angle 3.54815 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 184 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2102 (OUTLIER) cc_final: 0.0868 (mmt) REVERT: A 157 PHE cc_start: 0.6259 (m-10) cc_final: 0.5797 (m-10) REVERT: A 338 PHE cc_start: 0.7045 (m-80) cc_final: 0.6713 (m-80) REVERT: A 753 LEU cc_start: 0.7938 (tp) cc_final: 0.7634 (tp) REVERT: A 921 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8369 (mttt) REVERT: A 960 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7826 (m-40) REVERT: B 131 CYS cc_start: 0.2087 (OUTLIER) cc_final: 0.1757 (m) REVERT: B 160 TYR cc_start: 0.6661 (p90) cc_final: 0.6301 (p90) REVERT: B 269 TYR cc_start: 0.7674 (m-10) cc_final: 0.7361 (m-10) REVERT: B 978 ASN cc_start: 0.8286 (m-40) cc_final: 0.8000 (m-40) REVERT: D 153 MET cc_start: -0.0481 (ptp) cc_final: -0.1118 (pmm) REVERT: D 565 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: D 823 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: D 858 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (mm) REVERT: D 985 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: E 125 VAL cc_start: 0.0438 (OUTLIER) cc_final: 0.0121 (t) REVERT: G 83 MET cc_start: -0.0324 (mpp) cc_final: -0.0999 (tpt) outliers start: 89 outliers final: 51 residues processed: 258 average time/residue: 0.1751 time to fit residues: 76.3107 Evaluate side-chains 219 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 147 optimal weight: 40.0000 chunk 277 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN D 655 HIS D 901 GLN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.203689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133784 restraints weight = 42434.660| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.17 r_work: 0.3429 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29463 Z= 0.266 Angle : 0.753 21.250 40201 Z= 0.381 Chirality : 0.051 0.457 4619 Planarity : 0.005 0.060 5133 Dihedral : 5.837 57.642 4862 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 3.42 % Allowed : 17.84 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.14), residues: 3562 helix: 1.56 (0.20), residues: 672 sheet: 0.16 (0.17), residues: 867 loop : -1.18 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.029 0.002 TYR B 674 PHE 0.035 0.003 PHE A 970 TRP 0.024 0.002 TRP D 436 HIS 0.009 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00643 (29374) covalent geometry : angle 0.72197 (39976) SS BOND : bond 0.00535 ( 42) SS BOND : angle 1.67167 ( 84) hydrogen bonds : bond 0.06784 ( 1129) hydrogen bonds : angle 5.75495 ( 3090) link_BETA1-4 : bond 0.00330 ( 11) link_BETA1-4 : angle 1.50853 ( 33) link_NAG-ASN : bond 0.00862 ( 36) link_NAG-ASN : angle 3.89771 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 170 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7594 (t80) REVERT: A 239 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: A 484 GLU cc_start: 0.3463 (OUTLIER) cc_final: 0.3013 (tp30) REVERT: A 935 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6636 (tp40) REVERT: A 1138 TYR cc_start: 0.7845 (t80) cc_final: 0.7614 (t80) REVERT: B 131 CYS cc_start: 0.1917 (OUTLIER) cc_final: 0.1454 (m) REVERT: B 160 TYR cc_start: 0.6874 (p90) cc_final: 0.6361 (p90) REVERT: B 210 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6584 (tp) REVERT: B 269 TYR cc_start: 0.8343 (m-10) cc_final: 0.7783 (m-10) REVERT: B 369 TYR cc_start: 0.0235 (OUTLIER) cc_final: -0.0013 (m-80) REVERT: B 646 ARG cc_start: 0.7447 (mmm160) cc_final: 0.7153 (tpm170) REVERT: B 1138 TYR cc_start: 0.7338 (t80) cc_final: 0.6850 (m-80) REVERT: D 153 MET cc_start: -0.0648 (ptp) cc_final: -0.1356 (pmm) REVERT: D 231 ILE cc_start: 0.6660 (mp) cc_final: 0.6398 (tt) REVERT: D 565 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: D 1138 TYR cc_start: 0.6960 (t80) cc_final: 0.6725 (t80) REVERT: E 125 VAL cc_start: 0.1636 (OUTLIER) cc_final: 0.1274 (t) outliers start: 107 outliers final: 61 residues processed: 263 average time/residue: 0.1724 time to fit residues: 76.9018 Evaluate side-chains 215 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 193 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 133 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN D 954 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.206943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.154511 restraints weight = 42476.495| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.71 r_work: 0.3603 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29463 Z= 0.130 Angle : 0.612 20.386 40201 Z= 0.307 Chirality : 0.046 0.455 4619 Planarity : 0.004 0.055 5133 Dihedral : 5.254 56.105 4860 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 2.46 % Allowed : 18.55 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3562 helix: 2.12 (0.21), residues: 670 sheet: 0.37 (0.17), residues: 859 loop : -1.04 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.016 0.001 TYR A 351 PHE 0.027 0.001 PHE A 347 TRP 0.020 0.001 TRP D 436 HIS 0.012 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00295 (29374) covalent geometry : angle 0.57804 (39976) SS BOND : bond 0.00498 ( 42) SS BOND : angle 2.10222 ( 84) hydrogen bonds : bond 0.04870 ( 1129) hydrogen bonds : angle 5.38548 ( 3090) link_BETA1-4 : bond 0.00464 ( 11) link_BETA1-4 : angle 1.25454 ( 33) link_NAG-ASN : bond 0.00700 ( 36) link_NAG-ASN : angle 3.47003 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 161 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7384 (t80) REVERT: A 484 GLU cc_start: 0.3657 (OUTLIER) cc_final: 0.3021 (tp30) REVERT: A 921 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (mttt) REVERT: A 935 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6570 (tp40) REVERT: A 1138 TYR cc_start: 0.7685 (t80) cc_final: 0.7453 (t80) REVERT: B 131 CYS cc_start: 0.2047 (OUTLIER) cc_final: 0.1687 (m) REVERT: B 160 TYR cc_start: 0.6600 (p90) cc_final: 0.6149 (p90) REVERT: B 269 TYR cc_start: 0.7853 (m-10) cc_final: 0.7426 (m-10) REVERT: B 369 TYR cc_start: 0.0494 (OUTLIER) cc_final: 0.0236 (m-80) REVERT: B 902 MET cc_start: 0.7933 (tpt) cc_final: 0.7496 (tpt) REVERT: D 153 MET cc_start: -0.0830 (ptp) cc_final: -0.1165 (pmm) REVERT: D 673 SER cc_start: 0.8498 (p) cc_final: 0.8081 (m) REVERT: E 125 VAL cc_start: -0.0474 (OUTLIER) cc_final: -0.0734 (t) outliers start: 77 outliers final: 47 residues processed: 223 average time/residue: 0.1827 time to fit residues: 68.7029 Evaluate side-chains 201 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 169 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 350 optimal weight: 30.0000 chunk 307 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 954 GLN E 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.205334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135456 restraints weight = 42816.315| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.04 r_work: 0.3458 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 29463 Z= 0.308 Angle : 0.779 21.095 40201 Z= 0.394 Chirality : 0.052 0.480 4619 Planarity : 0.005 0.067 5133 Dihedral : 5.927 59.911 4860 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 2.91 % Allowed : 18.45 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.14), residues: 3562 helix: 1.38 (0.20), residues: 678 sheet: 0.13 (0.17), residues: 900 loop : -1.31 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 72 TYR 0.025 0.002 TYR B 279 PHE 0.026 0.003 PHE A 970 TRP 0.022 0.002 TRP D 436 HIS 0.019 0.003 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00749 (29374) covalent geometry : angle 0.74450 (39976) SS BOND : bond 0.00539 ( 42) SS BOND : angle 2.43884 ( 84) hydrogen bonds : bond 0.07000 ( 1129) hydrogen bonds : angle 5.77939 ( 3090) link_BETA1-4 : bond 0.00340 ( 11) link_BETA1-4 : angle 1.50028 ( 33) link_NAG-ASN : bond 0.00879 ( 36) link_NAG-ASN : angle 3.91396 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 155 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7191 (tp40) cc_final: 0.6168 (mm-40) REVERT: A 200 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7656 (t80) REVERT: A 423 TYR cc_start: 0.5263 (OUTLIER) cc_final: 0.3858 (t80) REVERT: A 484 GLU cc_start: 0.3463 (OUTLIER) cc_final: 0.2976 (tp30) REVERT: A 751 ASN cc_start: 0.8001 (m-40) cc_final: 0.7752 (m110) REVERT: A 921 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8641 (mttt) REVERT: A 935 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.6708 (tp40) REVERT: A 1138 TYR cc_start: 0.7861 (t80) cc_final: 0.7653 (t80) REVERT: B 131 CYS cc_start: 0.1959 (OUTLIER) cc_final: 0.1497 (m) REVERT: B 160 TYR cc_start: 0.6916 (p90) cc_final: 0.6329 (p90) REVERT: B 200 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.6346 (t80) REVERT: B 210 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6883 (tp) REVERT: B 269 TYR cc_start: 0.8415 (m-10) cc_final: 0.7872 (m-10) REVERT: B 369 TYR cc_start: 0.0500 (OUTLIER) cc_final: 0.0164 (m-80) REVERT: D 153 MET cc_start: -0.0847 (ptp) cc_final: -0.1061 (pmm) REVERT: D 673 SER cc_start: 0.8747 (p) cc_final: 0.8242 (m) REVERT: E 125 VAL cc_start: 0.1123 (OUTLIER) cc_final: 0.0784 (t) outliers start: 91 outliers final: 58 residues processed: 233 average time/residue: 0.1764 time to fit residues: 69.7058 Evaluate side-chains 209 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 347 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 340 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN D 954 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.203770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135866 restraints weight = 42419.519| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.81 r_work: 0.3434 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 29463 Z= 0.266 Angle : 0.720 20.762 40201 Z= 0.365 Chirality : 0.050 0.495 4619 Planarity : 0.005 0.061 5133 Dihedral : 5.979 58.841 4860 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 2.94 % Allowed : 18.77 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3562 helix: 1.73 (0.20), residues: 660 sheet: 0.08 (0.17), residues: 902 loop : -1.33 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 214 TYR 0.024 0.002 TYR B 279 PHE 0.027 0.002 PHE B 490 TRP 0.033 0.002 TRP A 64 HIS 0.010 0.002 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00650 (29374) covalent geometry : angle 0.68694 (39976) SS BOND : bond 0.00446 ( 42) SS BOND : angle 2.20269 ( 84) hydrogen bonds : bond 0.06191 ( 1129) hydrogen bonds : angle 5.67268 ( 3090) link_BETA1-4 : bond 0.00339 ( 11) link_BETA1-4 : angle 1.37630 ( 33) link_NAG-ASN : bond 0.00713 ( 36) link_NAG-ASN : angle 3.76337 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 155 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7574 (t80) REVERT: A 423 TYR cc_start: 0.4869 (OUTLIER) cc_final: 0.4095 (t80) REVERT: A 484 GLU cc_start: 0.3553 (OUTLIER) cc_final: 0.3042 (tp30) REVERT: A 751 ASN cc_start: 0.8093 (m-40) cc_final: 0.7870 (m110) REVERT: A 921 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8597 (mttt) REVERT: A 935 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6661 (tp40) REVERT: B 131 CYS cc_start: 0.1863 (OUTLIER) cc_final: 0.1444 (m) REVERT: B 160 TYR cc_start: 0.6816 (p90) cc_final: 0.6201 (p90) REVERT: B 200 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 210 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6908 (tp) REVERT: B 269 TYR cc_start: 0.8363 (m-10) cc_final: 0.7997 (m-10) REVERT: B 369 TYR cc_start: 0.0473 (OUTLIER) cc_final: 0.0154 (m-80) REVERT: B 902 MET cc_start: 0.8290 (tpt) cc_final: 0.7694 (tpt) REVERT: D 153 MET cc_start: -0.0705 (ptp) cc_final: -0.0991 (pmm) REVERT: D 200 TYR cc_start: 0.7290 (m-80) cc_final: 0.7047 (m-80) REVERT: D 265 TYR cc_start: 0.7185 (p90) cc_final: 0.6874 (p90) REVERT: D 390 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7919 (tt) REVERT: D 673 SER cc_start: 0.8700 (p) cc_final: 0.8250 (m) REVERT: E 125 VAL cc_start: 0.0644 (OUTLIER) cc_final: 0.0316 (t) REVERT: F 100 GLU cc_start: 0.1514 (OUTLIER) cc_final: -0.0611 (mp0) outliers start: 92 outliers final: 64 residues processed: 235 average time/residue: 0.1758 time to fit residues: 70.1223 Evaluate side-chains 217 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 141 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 270 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 690 GLN B 52 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 914 ASN D 954 GLN D 965 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.204226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.152157 restraints weight = 42074.294| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.75 r_work: 0.3566 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29463 Z= 0.134 Angle : 0.626 19.688 40201 Z= 0.315 Chirality : 0.046 0.486 4619 Planarity : 0.005 0.059 5133 Dihedral : 5.482 59.009 4860 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 2.17 % Allowed : 19.73 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.14), residues: 3562 helix: 2.12 (0.21), residues: 669 sheet: 0.10 (0.17), residues: 841 loop : -1.19 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.018 0.001 TYR A 351 PHE 0.025 0.002 PHE A 106 TRP 0.024 0.001 TRP D 436 HIS 0.013 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00311 (29374) covalent geometry : angle 0.59531 (39976) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.64012 ( 84) hydrogen bonds : bond 0.04900 ( 1129) hydrogen bonds : angle 5.40739 ( 3090) link_BETA1-4 : bond 0.00357 ( 11) link_BETA1-4 : angle 1.25103 ( 33) link_NAG-ASN : bond 0.00635 ( 36) link_NAG-ASN : angle 3.48399 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6923 (tp40) cc_final: 0.6121 (mm110) REVERT: A 200 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7563 (t80) REVERT: A 423 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.3660 (t80) REVERT: A 484 GLU cc_start: 0.3451 (OUTLIER) cc_final: 0.2919 (tp30) REVERT: A 556 ASN cc_start: 0.7458 (p0) cc_final: 0.7145 (t0) REVERT: A 935 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6664 (tp40) REVERT: B 131 CYS cc_start: 0.2201 (OUTLIER) cc_final: 0.1669 (m) REVERT: B 210 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6781 (tp) REVERT: B 211 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6942 (p0) REVERT: B 269 TYR cc_start: 0.8274 (m-10) cc_final: 0.8012 (m-10) REVERT: B 369 TYR cc_start: 0.0546 (OUTLIER) cc_final: 0.0220 (m-80) REVERT: B 646 ARG cc_start: 0.7437 (tpm170) cc_final: 0.7099 (tpm170) REVERT: B 902 MET cc_start: 0.8249 (tpt) cc_final: 0.7619 (tpt) REVERT: D 265 TYR cc_start: 0.7279 (p90) cc_final: 0.7042 (p90) REVERT: D 673 SER cc_start: 0.8639 (p) cc_final: 0.8234 (m) REVERT: D 900 MET cc_start: 0.8802 (mtm) cc_final: 0.8596 (mtp) REVERT: E 125 VAL cc_start: -0.0495 (OUTLIER) cc_final: -0.0745 (t) outliers start: 68 outliers final: 48 residues processed: 214 average time/residue: 0.1791 time to fit residues: 66.2629 Evaluate side-chains 206 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 91 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 346 optimal weight: 30.0000 chunk 204 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN D 613 GLN D 954 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.205941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152388 restraints weight = 42616.862| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.69 r_work: 0.3581 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29463 Z= 0.118 Angle : 0.608 19.231 40201 Z= 0.305 Chirality : 0.046 0.473 4619 Planarity : 0.005 0.058 5133 Dihedral : 5.220 58.844 4860 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 2.05 % Allowed : 20.08 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3562 helix: 2.25 (0.21), residues: 667 sheet: 0.25 (0.17), residues: 840 loop : -1.09 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 905 TYR 0.043 0.001 TYR A 351 PHE 0.026 0.001 PHE A 106 TRP 0.027 0.002 TRP D 436 HIS 0.009 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00268 (29374) covalent geometry : angle 0.57841 (39976) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.52512 ( 84) hydrogen bonds : bond 0.04445 ( 1129) hydrogen bonds : angle 5.29893 ( 3090) link_BETA1-4 : bond 0.00353 ( 11) link_BETA1-4 : angle 1.16977 ( 33) link_NAG-ASN : bond 0.00625 ( 36) link_NAG-ASN : angle 3.36795 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7818.15 seconds wall clock time: 135 minutes 1.41 seconds (8101.41 seconds total)