Starting phenix.real_space_refine on Thu Jun 26 22:16:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c2r_16397/06_2025/8c2r_16397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c2r_16397/06_2025/8c2r_16397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c2r_16397/06_2025/8c2r_16397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c2r_16397/06_2025/8c2r_16397.map" model { file = "/net/cci-nas-00/data/ceres_data/8c2r_16397/06_2025/8c2r_16397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c2r_16397/06_2025/8c2r_16397.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.022 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 130 5.16 5 C 19695 2.51 5 N 5085 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 1.85s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30928 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7844 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 8 Chain: "B" Number of atoms: 7917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7917 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 55, 'TRANS': 953} Chain breaks: 8 Chain: "C" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7933 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 8 Chain: "E" Number of atoms: 1640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Conformer: "B" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} bond proxies already assigned to first conformer: 1668 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "L" Number of atoms: 1640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Conformer: "B" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} bond proxies already assigned to first conformer: 1668 Chain: "R" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.43, per 1000 atoms: 0.63 Number of scatterers: 30928 At special positions: 0 Unit cell: (123.22, 159.58, 246.44, 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 130 16.00 O 6018 8.00 N 5085 7.00 C 19695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 144 " - pdb=" SG CYS R 200 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 709 " NAG-THR " NAG A1302 " - " THR A 124 " Time building additional restraints: 6.85 Conformation dependent library (CDL) restraints added in 4.1 seconds 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7242 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 69 sheets defined 22.3% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.999A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.159A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.724A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.063A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.783A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.176A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.592A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.076A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.112A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.038A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.884A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.071A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.694A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.106A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.688A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.753A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.962A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.835A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.526A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.559A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.044A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.710A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.965A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.108A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.796A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 214 No H-bonds generated for 'chain 'E' and resid 212 through 214' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 189 through 196 removed outlier: 4.082A pdb=" N GLY F 194 " --> pdb=" O SER F 190 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.537A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 214 No H-bonds generated for 'chain 'L' and resid 212 through 214' Processing helix chain 'R' and resid 86 through 90 Processing helix chain 'R' and resid 189 through 196 removed outlier: 4.510A pdb=" N GLY R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR R 195 " --> pdb=" O SER R 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.874A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.576A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.225A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.474A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.285A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.899A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.062A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.109A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.267A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.267A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.488A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.415A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.364A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.805A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.737A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.518A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.527A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.585A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.439A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (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 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.527A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.334A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.334A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.101A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.821A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.237A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.464A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.017A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.292A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.533A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.515A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.389A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.389A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.525A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.336A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU E 33 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.336A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.579A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 154 through 155 removed outlier: 4.316A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AF9, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.563A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR F 33 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS F 95 " --> pdb=" O TRP F 107 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP F 107 " --> pdb=" O CYS F 95 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG F 97 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.563A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR F 33 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.965A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP F 148 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.965A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP F 148 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 154 through 158 removed outlier: 4.559A pdb=" N TYR F 198 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.544A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.544A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.515A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.214A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'R' and resid 11 through 12 removed outlier: 4.071A pdb=" N TYR R 33 " --> pdb=" O ASP R 98 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET R 34 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 11 through 12 removed outlier: 6.783A pdb=" N CYS R 95 " --> pdb=" O TRP R 107 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP R 107 " --> pdb=" O CYS R 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG R 97 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 124 through 128 removed outlier: 3.830A pdb=" N GLY R 143 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL R 188 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP R 148 " --> pdb=" O TYR R 180 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR R 180 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 124 through 128 removed outlier: 3.830A pdb=" N GLY R 143 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL R 188 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP R 148 " --> pdb=" O TYR R 180 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR R 180 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 154 through 158 removed outlier: 3.558A pdb=" N THR R 209 " --> pdb=" O HIS R 204 " (cutoff:3.500A) 1397 hydrogen bonds defined for protein. 3838 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: 18.47 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8174 1.33 - 1.47: 9597 1.47 - 1.60: 13708 1.60 - 1.73: 1 1.73 - 1.87: 159 Bond restraints: 31639 Sorted by residual: bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.19e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.14e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.26e+00 bond pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.93e+00 ... (remaining 31634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 42335 2.84 - 5.67: 627 5.67 - 8.51: 58 8.51 - 11.35: 9 11.35 - 14.18: 4 Bond angle restraints: 43033 Sorted by residual: angle pdb=" C TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta sigma weight residual 109.75 121.90 -12.15 1.65e+00 3.67e-01 5.42e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 126.72 -12.82 1.80e+00 3.09e-01 5.07e+01 angle pdb=" CA TYR A 200 " pdb=" CB TYR A 200 " pdb=" CG TYR A 200 " ideal model delta sigma weight residual 113.90 125.31 -11.41 1.80e+00 3.09e-01 4.02e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.58 -14.18 2.30e+00 1.89e-01 3.80e+01 angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta sigma weight residual 110.43 100.38 10.05 1.63e+00 3.76e-01 3.80e+01 ... (remaining 43028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 18943 25.09 - 50.18: 562 50.18 - 75.27: 42 75.27 - 100.36: 11 100.36 - 125.45: 3 Dihedral angle restraints: 19561 sinusoidal: 8295 harmonic: 11266 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.25 -88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 177.81 -84.81 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -169.21 83.21 1 1.00e+01 1.00e-02 8.46e+01 ... (remaining 19558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.359: 4980 0.359 - 0.719: 4 0.719 - 1.078: 0 1.078 - 1.438: 0 1.438 - 1.797: 1 Chirality restraints: 4985 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.60 -1.80 2.00e-01 2.50e+01 8.07e+01 chirality pdb=" CB VAL F 188 " pdb=" CA VAL F 188 " pdb=" CG1 VAL F 188 " pdb=" CG2 VAL F 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CB THR B 167 " pdb=" CA THR B 167 " pdb=" OG1 THR B 167 " pdb=" CG2 THR B 167 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 4982 not shown) Planarity restraints: 5505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 106 " 0.054 2.00e-02 2.50e+03 1.07e-01 1.14e+02 pdb=" C ILE E 106 " -0.185 2.00e-02 2.50e+03 pdb=" O ILE E 106 " 0.071 2.00e-02 2.50e+03 pdb=" N LYS E 107 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 106 " 0.051 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C ILE L 106 " -0.179 2.00e-02 2.50e+03 pdb=" O ILE L 106 " 0.068 2.00e-02 2.50e+03 pdb=" N LYS L 107 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.064 2.00e-02 2.50e+03 5.58e-02 6.22e+01 pdb=" CG TYR B 495 " 0.136 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.010 2.00e-02 2.50e+03 ... (remaining 5502 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 37 2.49 - 3.09: 22105 3.09 - 3.69: 44819 3.69 - 4.30: 71004 4.30 - 4.90: 115664 Nonbonded interactions: 253629 Sorted by model distance: nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 1.882 3.040 nonbonded pdb=" OG1 THR R 155 " pdb=" OD1 ASN R 203 " model vdw 1.911 3.040 nonbonded pdb=" O TYR E 186 " pdb=" OH TYR E 192 " model vdw 2.025 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.060 3.040 nonbonded pdb=" OE2 GLU R 6 " pdb=" N CYS R 95 " model vdw 2.145 3.120 ... (remaining 253624 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 27 through 67 or resid 80 through 134 or resid 156 through \ 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 27 through 134 or resid 156 through 243 or resid 263 throu \ gh 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 67 or resid 80 through 134 or resid 156 through \ 243 or resid 263 through 1147 or resid 1301 through 1306)) } ncs_group { reference = (chain 'E' and (resid 1 through 193 or resid 195 through 214)) selection = (chain 'L' and (resid 1 through 193 or resid 195 through 214)) } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 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: 0.010 Normalize map: mean=0, sd=1: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 77.080 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.007 0.114 31717 Z= 0.294 Angle : 0.911 20.014 43221 Z= 0.515 Chirality : 0.065 1.797 4985 Planarity : 0.006 0.107 5488 Dihedral : 11.143 125.449 12184 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.52 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.13), residues: 3809 helix: 4.31 (0.17), residues: 695 sheet: 2.53 (0.15), residues: 970 loop : 0.45 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.004 TRP C 886 HIS 0.012 0.002 HIS B 66 PHE 0.103 0.004 PHE C 347 TYR 0.136 0.003 TYR B 495 ARG 0.031 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 17) link_NAG-ASN : angle 4.70555 ( 51) link_BETA1-4 : bond 0.00477 ( 15) link_BETA1-4 : angle 1.32442 ( 45) hydrogen bonds : bond 0.18019 ( 1313) hydrogen bonds : angle 8.15409 ( 3838) SS BOND : bond 0.00706 ( 45) SS BOND : angle 2.95636 ( 90) link_NAG-THR : bond 0.00404 ( 1) link_NAG-THR : angle 2.08436 ( 2) covalent geometry : bond 0.00682 (31639) covalent geometry : angle 0.88704 (43033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 862 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 133 PHE cc_start: 0.8703 (m-80) cc_final: 0.8297 (m-80) REVERT: A 164 ASN cc_start: 0.7980 (t0) cc_final: 0.7624 (t0) REVERT: A 306 PHE cc_start: 0.7713 (m-80) cc_final: 0.7283 (m-80) REVERT: A 408 ARG cc_start: 0.8163 (ppt170) cc_final: 0.7718 (ppt170) REVERT: A 420 ASP cc_start: 0.8330 (m-30) cc_final: 0.7972 (m-30) REVERT: A 464 PHE cc_start: 0.9021 (m-80) cc_final: 0.8725 (m-10) REVERT: A 658 ASN cc_start: 0.7862 (p0) cc_final: 0.7507 (p0) REVERT: A 659 SER cc_start: 0.8558 (p) cc_final: 0.8271 (m) REVERT: A 660 TYR cc_start: 0.8469 (m-80) cc_final: 0.7939 (m-80) REVERT: A 819 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 825 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8108 (mttp) REVERT: A 884 SER cc_start: 0.8448 (p) cc_final: 0.8083 (t) REVERT: A 1031 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7886 (mp0) REVERT: A 1034 LEU cc_start: 0.9053 (mp) cc_final: 0.8757 (mt) REVERT: A 1072 GLU cc_start: 0.7896 (pm20) cc_final: 0.7682 (pm20) REVERT: B 120 VAL cc_start: 0.8184 (t) cc_final: 0.7969 (m) REVERT: B 306 PHE cc_start: 0.8906 (m-80) cc_final: 0.8660 (m-80) REVERT: B 309 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 410 ILE cc_start: 0.8974 (mm) cc_final: 0.8548 (pp) REVERT: B 508 TYR cc_start: 0.7588 (m-10) cc_final: 0.7166 (m-80) REVERT: B 574 ASP cc_start: 0.7393 (p0) cc_final: 0.7191 (t0) REVERT: B 584 ILE cc_start: 0.8788 (mp) cc_final: 0.8458 (mp) REVERT: B 586 ASP cc_start: 0.7689 (m-30) cc_final: 0.7444 (m-30) REVERT: B 773 GLU cc_start: 0.8209 (tt0) cc_final: 0.7936 (tm-30) REVERT: B 776 LYS cc_start: 0.8419 (tttp) cc_final: 0.8026 (ttmt) REVERT: B 868 GLU cc_start: 0.7813 (mp0) cc_final: 0.7591 (mp0) REVERT: B 949 GLN cc_start: 0.8186 (tp40) cc_final: 0.7945 (mm-40) REVERT: B 973 ILE cc_start: 0.9148 (pt) cc_final: 0.8623 (mm) REVERT: B 990 GLU cc_start: 0.7665 (tt0) cc_final: 0.7239 (tm-30) REVERT: B 992 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7153 (mm110) REVERT: B 1139 ASP cc_start: 0.7485 (t0) cc_final: 0.7118 (t0) REVERT: C 239 GLN cc_start: 0.7983 (tt0) cc_final: 0.7771 (tt0) REVERT: C 305 SER cc_start: 0.8403 (p) cc_final: 0.8174 (p) REVERT: C 307 THR cc_start: 0.8435 (p) cc_final: 0.8009 (t) REVERT: C 394 ASN cc_start: 0.7835 (t0) cc_final: 0.7380 (t0) REVERT: C 402 ILE cc_start: 0.8670 (pt) cc_final: 0.8451 (pt) REVERT: C 418 ILE cc_start: 0.8662 (pt) cc_final: 0.7496 (pt) REVERT: C 451 TYR cc_start: 0.7572 (m-80) cc_final: 0.7167 (m-10) REVERT: C 516 GLU cc_start: 0.7452 (pp20) cc_final: 0.6825 (tm-30) REVERT: C 517 LEU cc_start: 0.8680 (mm) cc_final: 0.8439 (mm) REVERT: C 569 ILE cc_start: 0.8025 (pt) cc_final: 0.7775 (mp) REVERT: C 581 THR cc_start: 0.8741 (m) cc_final: 0.8510 (t) REVERT: C 735 SER cc_start: 0.8851 (t) cc_final: 0.8593 (p) REVERT: C 983 ARG cc_start: 0.7227 (mtp180) cc_final: 0.7024 (tpp80) REVERT: C 987 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7407 (Cg_endo) REVERT: C 1038 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8096 (mptp) REVERT: C 1045 LYS cc_start: 0.7545 (tptp) cc_final: 0.6755 (mmmt) REVERT: E 46 LEU cc_start: 0.8510 (tp) cc_final: 0.8176 (tm) REVERT: E 75 ILE cc_start: 0.8562 (mt) cc_final: 0.8250 (mt) REVERT: E 79 GLU cc_start: 0.6703 (mp0) cc_final: 0.6386 (mp0) REVERT: E 89 GLN cc_start: 0.8703 (pp30) cc_final: 0.8370 (pp30) REVERT: E 90 GLN cc_start: 0.8464 (pp30) cc_final: 0.8260 (pp30) REVERT: F 13 GLN cc_start: 0.7669 (pm20) cc_final: 0.7468 (pm20) REVERT: F 25 SER cc_start: 0.8799 (m) cc_final: 0.7959 (p) REVERT: F 34 MET cc_start: 0.8643 (mmm) cc_final: 0.8400 (mmm) REVERT: F 124 SER cc_start: 0.8417 (m) cc_final: 0.7978 (p) REVERT: F 142 LEU cc_start: 0.7784 (pp) cc_final: 0.7561 (pp) REVERT: F 154 VAL cc_start: 0.8633 (p) cc_final: 0.8284 (m) REVERT: L 42 GLN cc_start: 0.7747 (mt0) cc_final: 0.7509 (mt0) REVERT: L 47 LEU cc_start: 0.8154 (mt) cc_final: 0.7909 (mm) REVERT: L 72 THR cc_start: 0.8405 (m) cc_final: 0.8168 (t) REVERT: L 175 LEU cc_start: 0.7854 (tt) cc_final: 0.7383 (mt) REVERT: R 56 SER cc_start: 0.8616 (m) cc_final: 0.8264 (t) REVERT: R 77 THR cc_start: 0.8336 (m) cc_final: 0.8024 (m) REVERT: R 79 TYR cc_start: 0.8318 (m-80) cc_final: 0.8048 (m-80) REVERT: R 142 LEU cc_start: 0.7651 (pt) cc_final: 0.7391 (pt) REVERT: R 149 TYR cc_start: 0.7770 (p90) cc_final: 0.6817 (p90) REVERT: R 163 LEU cc_start: 0.8003 (tp) cc_final: 0.7750 (tp) outliers start: 0 outliers final: 0 residues processed: 862 average time/residue: 1.2257 time to fit residues: 1272.2486 Evaluate side-chains 726 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 726 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.0050 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 348 optimal weight: 7.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 185 ASN A 207 HIS A 360 ASN A 414 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1074 ASN B 66 HIS B 185 ASN B 354 ASN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN B 935 GLN B1108 ASN C 207 HIS C 613 GLN C 787 GLN C 804 GLN C 965 GLN C1074 ASN C1098 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 168 HIS L 38 GLN R 109 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.169979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134114 restraints weight = 59481.173| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.59 r_work: 0.3650 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 31717 Z= 0.167 Angle : 0.656 12.930 43221 Z= 0.350 Chirality : 0.047 0.579 4985 Planarity : 0.005 0.060 5488 Dihedral : 6.040 100.546 5257 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.31 % Allowed : 12.93 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.13), residues: 3809 helix: 2.91 (0.18), residues: 714 sheet: 2.10 (0.15), residues: 984 loop : 0.17 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 886 HIS 0.005 0.001 HIS B1064 PHE 0.027 0.002 PHE B 759 TYR 0.047 0.002 TYR B 495 ARG 0.012 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 17) link_NAG-ASN : angle 2.96892 ( 51) link_BETA1-4 : bond 0.00385 ( 15) link_BETA1-4 : angle 1.11692 ( 45) hydrogen bonds : bond 0.05642 ( 1313) hydrogen bonds : angle 6.34047 ( 3838) SS BOND : bond 0.00367 ( 45) SS BOND : angle 2.36051 ( 90) link_NAG-THR : bond 0.00158 ( 1) link_NAG-THR : angle 1.14805 ( 2) covalent geometry : bond 0.00372 (31639) covalent geometry : angle 0.63888 (43033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 734 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8685 (m-80) cc_final: 0.7761 (m-80) REVERT: A 164 ASN cc_start: 0.8213 (t0) cc_final: 0.7885 (t0) REVERT: A 306 PHE cc_start: 0.7908 (m-80) cc_final: 0.7480 (m-80) REVERT: A 347 PHE cc_start: 0.8479 (m-80) cc_final: 0.7954 (m-80) REVERT: A 420 ASP cc_start: 0.8526 (m-30) cc_final: 0.8081 (m-30) REVERT: A 450 ASN cc_start: 0.8547 (m110) cc_final: 0.8308 (p0) REVERT: A 567 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7575 (mtt180) REVERT: A 659 SER cc_start: 0.8574 (p) cc_final: 0.8354 (m) REVERT: A 718 PHE cc_start: 0.8633 (p90) cc_final: 0.8409 (p90) REVERT: A 740 MET cc_start: 0.8528 (mmm) cc_final: 0.8254 (tpt) REVERT: A 825 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8385 (mttp) REVERT: A 904 TYR cc_start: 0.7619 (t80) cc_final: 0.7382 (t80) REVERT: A 1072 GLU cc_start: 0.8377 (pm20) cc_final: 0.8136 (pm20) REVERT: A 1091 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7736 (mtm-85) REVERT: B 309 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 347 PHE cc_start: 0.7732 (m-80) cc_final: 0.7525 (m-80) REVERT: B 349 SER cc_start: 0.8020 (m) cc_final: 0.7789 (p) REVERT: B 357 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7765 (tpt-90) REVERT: B 410 ILE cc_start: 0.9007 (mm) cc_final: 0.8687 (pp) REVERT: B 466 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7771 (ttm-80) REVERT: B 498 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.8098 (mpt90) REVERT: B 508 TYR cc_start: 0.7726 (m-10) cc_final: 0.7402 (m-80) REVERT: B 586 ASP cc_start: 0.8000 (m-30) cc_final: 0.7792 (m-30) REVERT: B 619 GLU cc_start: 0.7470 (mp0) cc_final: 0.7194 (mp0) REVERT: B 773 GLU cc_start: 0.8100 (tt0) cc_final: 0.7898 (tm-30) REVERT: B 973 ILE cc_start: 0.9143 (pt) cc_final: 0.8799 (mm) REVERT: B 983 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7905 (mtm-85) REVERT: B 990 GLU cc_start: 0.8055 (tt0) cc_final: 0.7393 (tm-30) REVERT: C 307 THR cc_start: 0.8582 (p) cc_final: 0.8147 (t) REVERT: C 394 ASN cc_start: 0.7746 (t0) cc_final: 0.7503 (t0) REVERT: C 420 ASP cc_start: 0.7716 (p0) cc_final: 0.7447 (p0) REVERT: C 442 ASP cc_start: 0.7608 (m-30) cc_final: 0.7380 (t0) REVERT: C 493 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7676 (mtp85) REVERT: C 516 GLU cc_start: 0.7955 (pp20) cc_final: 0.7391 (tm-30) REVERT: C 559 PHE cc_start: 0.7335 (m-80) cc_final: 0.6981 (m-80) REVERT: C 584 ILE cc_start: 0.8901 (mp) cc_final: 0.8652 (mm) REVERT: C 811 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7799 (mmtm) REVERT: C 990 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7196 (tm-30) REVERT: C 1045 LYS cc_start: 0.7939 (tptp) cc_final: 0.7349 (mmmt) REVERT: E 6 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: E 46 LEU cc_start: 0.8699 (tp) cc_final: 0.8378 (tm) REVERT: E 75 ILE cc_start: 0.8719 (mt) cc_final: 0.8358 (mt) REVERT: E 79 GLU cc_start: 0.7028 (mp0) cc_final: 0.6643 (mp0) REVERT: E 89 GLN cc_start: 0.8763 (pp30) cc_final: 0.8228 (pp30) REVERT: E 90 GLN cc_start: 0.8130 (pp30) cc_final: 0.7827 (pp30) REVERT: F 13 GLN cc_start: 0.7688 (pm20) cc_final: 0.7432 (pm20) REVERT: F 25 SER cc_start: 0.8712 (m) cc_final: 0.7963 (p) REVERT: F 34 MET cc_start: 0.8526 (mmm) cc_final: 0.8310 (tpp) REVERT: F 59 TYR cc_start: 0.8063 (m-80) cc_final: 0.7756 (m-80) REVERT: F 106 TYR cc_start: 0.7984 (m-80) cc_final: 0.7481 (m-10) REVERT: F 124 SER cc_start: 0.8355 (m) cc_final: 0.7735 (p) REVERT: F 142 LEU cc_start: 0.7635 (pp) cc_final: 0.7370 (pp) REVERT: L 11 LEU cc_start: 0.8414 (tp) cc_final: 0.7622 (mt) REVERT: L 37 GLN cc_start: 0.8591 (tt0) cc_final: 0.8358 (tt0) REVERT: L 42 GLN cc_start: 0.7741 (mt0) cc_final: 0.7501 (mt0) REVERT: L 89 GLN cc_start: 0.8063 (tm130) cc_final: 0.7804 (tm130) REVERT: L 175 LEU cc_start: 0.7870 (tt) cc_final: 0.7453 (mp) REVERT: L 181 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (pt) REVERT: R 4 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8435 (tt) REVERT: R 45 LEU cc_start: 0.8588 (mt) cc_final: 0.8245 (mp) REVERT: R 56 SER cc_start: 0.8526 (m) cc_final: 0.8060 (t) REVERT: R 59 TYR cc_start: 0.7882 (m-80) cc_final: 0.7497 (m-80) REVERT: R 77 THR cc_start: 0.8117 (m) cc_final: 0.7697 (m) REVERT: R 79 TYR cc_start: 0.8227 (m-80) cc_final: 0.7807 (m-80) REVERT: R 149 TYR cc_start: 0.7630 (p90) cc_final: 0.6549 (p90) REVERT: R 163 LEU cc_start: 0.8194 (tp) cc_final: 0.7885 (tp) outliers start: 78 outliers final: 26 residues processed: 766 average time/residue: 1.2195 time to fit residues: 1138.4711 Evaluate side-chains 715 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 685 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 182 optimal weight: 2.9990 chunk 271 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 chunk 329 optimal weight: 9.9990 chunk 253 optimal weight: 0.0030 chunk 152 optimal weight: 0.8980 chunk 288 optimal weight: 0.3980 chunk 230 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1074 ASN B 66 HIS B 354 ASN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C 437 ASN C 613 GLN C 755 GLN C 787 GLN C 804 GLN C 965 GLN C1005 GLN C1058 HIS C1074 ASN C1134 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.169024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132294 restraints weight = 60665.808| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.55 r_work: 0.3629 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 31717 Z= 0.178 Angle : 0.624 13.575 43221 Z= 0.326 Chirality : 0.046 0.560 4985 Planarity : 0.005 0.051 5488 Dihedral : 5.818 93.442 5257 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.37 % Allowed : 14.29 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 3809 helix: 2.43 (0.18), residues: 730 sheet: 1.68 (0.15), residues: 990 loop : 0.05 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 107 HIS 0.006 0.001 HIS B1058 PHE 0.024 0.002 PHE B 970 TYR 0.038 0.002 TYR B 495 ARG 0.012 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 17) link_NAG-ASN : angle 2.98142 ( 51) link_BETA1-4 : bond 0.00273 ( 15) link_BETA1-4 : angle 1.12538 ( 45) hydrogen bonds : bond 0.05314 ( 1313) hydrogen bonds : angle 5.96224 ( 3838) SS BOND : bond 0.00415 ( 45) SS BOND : angle 2.29634 ( 90) link_NAG-THR : bond 0.00194 ( 1) link_NAG-THR : angle 1.45140 ( 2) covalent geometry : bond 0.00409 (31639) covalent geometry : angle 0.60655 (43033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 704 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.8641 (m) cc_final: 0.8423 (m) REVERT: A 133 PHE cc_start: 0.8703 (m-80) cc_final: 0.7879 (m-80) REVERT: A 164 ASN cc_start: 0.8198 (t0) cc_final: 0.7824 (t0) REVERT: A 347 PHE cc_start: 0.8656 (m-80) cc_final: 0.8228 (m-80) REVERT: A 423 TYR cc_start: 0.7980 (t80) cc_final: 0.7640 (t80) REVERT: A 498 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7671 (mmm-85) REVERT: A 567 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7715 (mtt180) REVERT: A 659 SER cc_start: 0.8591 (p) cc_final: 0.8358 (m) REVERT: A 718 PHE cc_start: 0.8753 (p90) cc_final: 0.8456 (p90) REVERT: A 740 MET cc_start: 0.8475 (mmm) cc_final: 0.8168 (tpt) REVERT: A 764 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8526 (ttpp) REVERT: A 825 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8470 (mttm) REVERT: A 950 ASP cc_start: 0.8106 (m-30) cc_final: 0.7900 (m-30) REVERT: A 1072 GLU cc_start: 0.8401 (pm20) cc_final: 0.8150 (pm20) REVERT: A 1091 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7849 (mtm-85) REVERT: A 1107 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7462 (mtm-85) REVERT: B 190 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7591 (mtp85) REVERT: B 220 PHE cc_start: 0.8019 (t80) cc_final: 0.7737 (t80) REVERT: B 229 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7515 (mt) REVERT: B 309 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8159 (mm-30) REVERT: B 347 PHE cc_start: 0.7795 (m-80) cc_final: 0.7591 (m-80) REVERT: B 349 SER cc_start: 0.8067 (m) cc_final: 0.7808 (p) REVERT: B 357 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7824 (tpt-90) REVERT: B 398 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7435 (p0) REVERT: B 410 ILE cc_start: 0.8997 (mm) cc_final: 0.8681 (pp) REVERT: B 498 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8087 (mpt-90) REVERT: B 508 TYR cc_start: 0.7741 (m-10) cc_final: 0.7514 (m-80) REVERT: B 586 ASP cc_start: 0.8013 (m-30) cc_final: 0.7766 (m-30) REVERT: B 748 GLU cc_start: 0.8005 (mp0) cc_final: 0.7701 (pm20) REVERT: B 904 TYR cc_start: 0.7957 (m-10) cc_final: 0.7741 (m-10) REVERT: B 973 ILE cc_start: 0.9126 (pt) cc_final: 0.8805 (mm) REVERT: B 980 ILE cc_start: 0.8637 (mt) cc_final: 0.8416 (mm) REVERT: B 990 GLU cc_start: 0.7992 (tt0) cc_final: 0.7349 (tm-30) REVERT: C 493 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7613 (mtp85) REVERT: C 516 GLU cc_start: 0.7968 (pp20) cc_final: 0.7493 (tm-30) REVERT: C 517 LEU cc_start: 0.8616 (mm) cc_final: 0.8002 (mt) REVERT: C 559 PHE cc_start: 0.7547 (m-80) cc_final: 0.7241 (m-80) REVERT: C 584 ILE cc_start: 0.8869 (mp) cc_final: 0.8618 (mm) REVERT: C 755 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7550 (mp-120) REVERT: C 884 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 904 TYR cc_start: 0.8164 (m-10) cc_final: 0.7840 (m-10) REVERT: C 990 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7186 (tm-30) REVERT: C 1045 LYS cc_start: 0.7943 (tptp) cc_final: 0.7413 (mmmt) REVERT: E 33 LEU cc_start: 0.8347 (tp) cc_final: 0.8083 (tp) REVERT: E 46 LEU cc_start: 0.8683 (tp) cc_final: 0.8447 (tp) REVERT: E 79 GLU cc_start: 0.7028 (mp0) cc_final: 0.6637 (mp0) REVERT: E 89 GLN cc_start: 0.8809 (pp30) cc_final: 0.8215 (pp30) REVERT: E 90 GLN cc_start: 0.8277 (pp30) cc_final: 0.7966 (pp30) REVERT: F 25 SER cc_start: 0.8623 (m) cc_final: 0.7897 (p) REVERT: F 59 TYR cc_start: 0.8184 (m-80) cc_final: 0.7819 (m-80) REVERT: F 106 TYR cc_start: 0.8067 (m-80) cc_final: 0.7639 (m-10) REVERT: F 124 SER cc_start: 0.8239 (m) cc_final: 0.7615 (p) REVERT: F 142 LEU cc_start: 0.7686 (pp) cc_final: 0.7382 (pp) REVERT: F 179 LEU cc_start: 0.7103 (mm) cc_final: 0.6828 (mt) REVERT: L 42 GLN cc_start: 0.7855 (mt0) cc_final: 0.7605 (mt0) REVERT: L 89 GLN cc_start: 0.8181 (tm130) cc_final: 0.7911 (tm130) REVERT: L 175 LEU cc_start: 0.7943 (tt) cc_final: 0.7627 (mp) REVERT: L 181 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7626 (pt) REVERT: R 4 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8547 (tt) REVERT: R 11 LEU cc_start: 0.8356 (mt) cc_final: 0.8091 (tp) REVERT: R 45 LEU cc_start: 0.8533 (mt) cc_final: 0.8252 (mp) REVERT: R 56 SER cc_start: 0.8547 (m) cc_final: 0.8089 (t) REVERT: R 59 TYR cc_start: 0.7907 (m-80) cc_final: 0.7631 (m-80) REVERT: R 63 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8458 (p) REVERT: R 163 LEU cc_start: 0.8165 (tp) cc_final: 0.7721 (pt) outliers start: 114 outliers final: 50 residues processed: 759 average time/residue: 1.2175 time to fit residues: 1116.0702 Evaluate side-chains 749 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 689 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 363 optimal weight: 7.9990 chunk 267 optimal weight: 0.0030 chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 367 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1074 ASN B 66 HIS B 354 ASN B 532 ASN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 207 HIS C 613 GLN C 955 ASN C 965 GLN C1005 GLN C1074 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.169373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.132452 restraints weight = 63844.513| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.85 r_work: 0.3613 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31717 Z= 0.138 Angle : 0.599 12.887 43221 Z= 0.309 Chirality : 0.044 0.371 4985 Planarity : 0.004 0.057 5488 Dihedral : 5.507 85.617 5257 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.40 % Allowed : 15.56 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.13), residues: 3809 helix: 2.28 (0.19), residues: 736 sheet: 1.46 (0.15), residues: 1040 loop : -0.03 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 107 HIS 0.004 0.001 HIS B1058 PHE 0.024 0.001 PHE B 970 TYR 0.029 0.002 TYR B 495 ARG 0.013 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 17) link_NAG-ASN : angle 2.33015 ( 51) link_BETA1-4 : bond 0.00284 ( 15) link_BETA1-4 : angle 1.14511 ( 45) hydrogen bonds : bond 0.04676 ( 1313) hydrogen bonds : angle 5.71483 ( 3838) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.97954 ( 90) link_NAG-THR : bond 0.00220 ( 1) link_NAG-THR : angle 1.94220 ( 2) covalent geometry : bond 0.00311 (31639) covalent geometry : angle 0.58622 (43033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 710 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.8544 (m) cc_final: 0.8328 (m) REVERT: A 133 PHE cc_start: 0.8658 (m-80) cc_final: 0.7862 (m-80) REVERT: A 164 ASN cc_start: 0.8062 (t0) cc_final: 0.7474 (t0) REVERT: A 165 ASN cc_start: 0.7587 (m-40) cc_final: 0.7288 (m110) REVERT: A 347 PHE cc_start: 0.8687 (m-80) cc_final: 0.8215 (m-80) REVERT: A 423 TYR cc_start: 0.7916 (t80) cc_final: 0.7489 (t80) REVERT: A 498 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7699 (mmm-85) REVERT: A 567 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7514 (mtt180) REVERT: A 659 SER cc_start: 0.8460 (p) cc_final: 0.8254 (m) REVERT: A 718 PHE cc_start: 0.8645 (p90) cc_final: 0.8381 (p90) REVERT: A 740 MET cc_start: 0.8204 (mmm) cc_final: 0.7883 (tpt) REVERT: A 825 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8376 (mttm) REVERT: A 904 TYR cc_start: 0.7235 (t80) cc_final: 0.6958 (t80) REVERT: A 1072 GLU cc_start: 0.8131 (pm20) cc_final: 0.7877 (pm20) REVERT: A 1107 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7142 (mtm-85) REVERT: B 52 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7856 (tp40) REVERT: B 190 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7246 (mtp85) REVERT: B 220 PHE cc_start: 0.8020 (t80) cc_final: 0.7783 (t80) REVERT: B 229 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7320 (mt) REVERT: B 309 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 347 PHE cc_start: 0.7683 (m-80) cc_final: 0.6277 (m-80) REVERT: B 349 SER cc_start: 0.8034 (m) cc_final: 0.7766 (p) REVERT: B 357 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7721 (tpt-90) REVERT: B 410 ILE cc_start: 0.8969 (mm) cc_final: 0.8624 (pp) REVERT: B 508 TYR cc_start: 0.7647 (m-80) cc_final: 0.7380 (m-80) REVERT: B 586 ASP cc_start: 0.7658 (m-30) cc_final: 0.7444 (m-30) REVERT: B 970 PHE cc_start: 0.8240 (m-80) cc_final: 0.7954 (m-10) REVERT: B 973 ILE cc_start: 0.8896 (pt) cc_final: 0.8511 (mm) REVERT: B 990 GLU cc_start: 0.7629 (tt0) cc_final: 0.7093 (tm-30) REVERT: C 235 ILE cc_start: 0.8653 (mt) cc_final: 0.8333 (tt) REVERT: C 269 TYR cc_start: 0.8327 (m-80) cc_final: 0.7884 (m-80) REVERT: C 451 TYR cc_start: 0.7459 (m-80) cc_final: 0.7241 (m-80) REVERT: C 493 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7407 (mtp85) REVERT: C 516 GLU cc_start: 0.7651 (pp20) cc_final: 0.7187 (tm-30) REVERT: C 517 LEU cc_start: 0.8565 (mm) cc_final: 0.7937 (mt) REVERT: C 543 PHE cc_start: 0.8467 (m-10) cc_final: 0.8245 (m-10) REVERT: C 574 ASP cc_start: 0.7717 (t0) cc_final: 0.7483 (p0) REVERT: C 584 ILE cc_start: 0.8791 (mp) cc_final: 0.8524 (mm) REVERT: C 811 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7818 (mptp) REVERT: C 950 ASP cc_start: 0.7333 (m-30) cc_final: 0.7054 (m-30) REVERT: C 990 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6889 (tm-30) REVERT: C 1045 LYS cc_start: 0.7732 (tptp) cc_final: 0.7165 (mmmt) REVERT: E 46 LEU cc_start: 0.8584 (tp) cc_final: 0.8338 (tp) REVERT: E 79 GLU cc_start: 0.6895 (mp0) cc_final: 0.6533 (mp0) REVERT: E 89 GLN cc_start: 0.8772 (pp30) cc_final: 0.8077 (pp30) REVERT: E 90 GLN cc_start: 0.8125 (pp30) cc_final: 0.7822 (pp30) REVERT: F 25 SER cc_start: 0.8552 (m) cc_final: 0.7813 (p) REVERT: F 59 TYR cc_start: 0.8112 (m-80) cc_final: 0.7733 (m-80) REVERT: F 106 TYR cc_start: 0.7971 (m-80) cc_final: 0.7612 (m-10) REVERT: F 124 SER cc_start: 0.8052 (m) cc_final: 0.7378 (p) REVERT: F 142 LEU cc_start: 0.7655 (pp) cc_final: 0.7332 (pp) REVERT: F 179 LEU cc_start: 0.7030 (mm) cc_final: 0.6649 (mt) REVERT: L 11 LEU cc_start: 0.8342 (tp) cc_final: 0.7613 (mt) REVERT: L 42 GLN cc_start: 0.7861 (mt0) cc_final: 0.7590 (mt0) REVERT: L 89 GLN cc_start: 0.8139 (tm130) cc_final: 0.7840 (tm130) REVERT: L 175 LEU cc_start: 0.7961 (tt) cc_final: 0.7603 (mp) REVERT: L 181 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7450 (pt) REVERT: R 4 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8576 (tt) REVERT: R 37 VAL cc_start: 0.8638 (p) cc_final: 0.8265 (m) REVERT: R 45 LEU cc_start: 0.8445 (mt) cc_final: 0.8172 (mp) REVERT: R 56 SER cc_start: 0.8403 (m) cc_final: 0.7764 (t) REVERT: R 63 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8400 (p) REVERT: R 93 TYR cc_start: 0.8365 (m-80) cc_final: 0.8075 (m-80) REVERT: R 149 TYR cc_start: 0.7726 (p90) cc_final: 0.6628 (p90) REVERT: R 163 LEU cc_start: 0.8083 (tp) cc_final: 0.7784 (tp) outliers start: 115 outliers final: 50 residues processed: 764 average time/residue: 1.1960 time to fit residues: 1114.1759 Evaluate side-chains 745 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 689 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 275 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 172 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 344 optimal weight: 9.9990 chunk 357 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN A1135 ASN B 66 HIS B 354 ASN B 532 ASN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 207 HIS C 556 ASN C 613 GLN C 703 ASN C 955 ASN C 965 GLN C1098 ASN E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.167249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129805 restraints weight = 67244.057| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.96 r_work: 0.3575 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31717 Z= 0.219 Angle : 0.637 12.474 43221 Z= 0.330 Chirality : 0.046 0.330 4985 Planarity : 0.005 0.078 5488 Dihedral : 5.474 74.662 5257 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.76 % Allowed : 15.79 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.13), residues: 3809 helix: 2.12 (0.19), residues: 723 sheet: 1.28 (0.15), residues: 1040 loop : -0.20 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 64 HIS 0.010 0.001 HIS B1058 PHE 0.024 0.002 PHE C 888 TYR 0.031 0.002 TYR C 265 ARG 0.013 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 17) link_NAG-ASN : angle 2.32038 ( 51) link_BETA1-4 : bond 0.00301 ( 15) link_BETA1-4 : angle 1.11045 ( 45) hydrogen bonds : bond 0.05151 ( 1313) hydrogen bonds : angle 5.75794 ( 3838) SS BOND : bond 0.00433 ( 45) SS BOND : angle 2.33297 ( 90) link_NAG-THR : bond 0.00249 ( 1) link_NAG-THR : angle 2.26857 ( 2) covalent geometry : bond 0.00509 (31639) covalent geometry : angle 0.62295 (43033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 703 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.8595 (m) cc_final: 0.8376 (m) REVERT: A 132 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 133 PHE cc_start: 0.8679 (m-80) cc_final: 0.7963 (m-80) REVERT: A 164 ASN cc_start: 0.8074 (t0) cc_final: 0.7483 (t0) REVERT: A 298 GLU cc_start: 0.8171 (tt0) cc_final: 0.7925 (tt0) REVERT: A 347 PHE cc_start: 0.8769 (m-80) cc_final: 0.8368 (m-80) REVERT: A 377 PHE cc_start: 0.7976 (t80) cc_final: 0.7675 (t80) REVERT: A 423 TYR cc_start: 0.7933 (t80) cc_final: 0.7530 (t80) REVERT: A 467 ASP cc_start: 0.7691 (t0) cc_final: 0.7413 (t0) REVERT: A 498 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7709 (mmm-85) REVERT: A 567 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7533 (mtt180) REVERT: A 659 SER cc_start: 0.8509 (p) cc_final: 0.8269 (m) REVERT: A 718 PHE cc_start: 0.8772 (p90) cc_final: 0.8458 (p90) REVERT: A 740 MET cc_start: 0.8232 (mmm) cc_final: 0.7884 (tpt) REVERT: A 825 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8318 (mttp) REVERT: A 950 ASP cc_start: 0.7854 (m-30) cc_final: 0.7576 (m-30) REVERT: A 1019 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7966 (tpt170) REVERT: A 1072 GLU cc_start: 0.8150 (pm20) cc_final: 0.7931 (pm20) REVERT: B 52 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7938 (tp40) REVERT: B 129 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7784 (mppt) REVERT: B 190 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7367 (mtp85) REVERT: B 220 PHE cc_start: 0.8093 (t80) cc_final: 0.7822 (t80) REVERT: B 309 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 347 PHE cc_start: 0.7670 (m-80) cc_final: 0.7170 (m-80) REVERT: B 410 ILE cc_start: 0.8997 (mm) cc_final: 0.8633 (pp) REVERT: B 505 HIS cc_start: 0.8063 (m-70) cc_final: 0.7795 (m-70) REVERT: B 508 TYR cc_start: 0.7580 (m-80) cc_final: 0.7343 (m-80) REVERT: B 586 ASP cc_start: 0.7695 (m-30) cc_final: 0.7474 (m-30) REVERT: B 748 GLU cc_start: 0.7745 (mp0) cc_final: 0.7510 (pm20) REVERT: B 773 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: B 825 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8444 (ttmm) REVERT: B 950 ASP cc_start: 0.7709 (m-30) cc_final: 0.7342 (m-30) REVERT: B 973 ILE cc_start: 0.8851 (pt) cc_final: 0.8480 (mm) REVERT: B 990 GLU cc_start: 0.7747 (tt0) cc_final: 0.7183 (tm-30) REVERT: C 108 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7427 (t) REVERT: C 269 TYR cc_start: 0.8373 (m-80) cc_final: 0.8062 (m-80) REVERT: C 493 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7422 (mtp85) REVERT: C 516 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: C 517 LEU cc_start: 0.8654 (mm) cc_final: 0.8097 (mt) REVERT: C 584 ILE cc_start: 0.8773 (mp) cc_final: 0.8514 (mm) REVERT: C 748 GLU cc_start: 0.7997 (pm20) cc_final: 0.7672 (mp0) REVERT: C 900 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: C 950 ASP cc_start: 0.7518 (m-30) cc_final: 0.7268 (m-30) REVERT: C 990 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6959 (tm-30) REVERT: C 1045 LYS cc_start: 0.7642 (tptp) cc_final: 0.7052 (mtpt) REVERT: E 46 LEU cc_start: 0.8603 (tp) cc_final: 0.8343 (tp) REVERT: E 78 LEU cc_start: 0.7436 (mt) cc_final: 0.7067 (mt) REVERT: E 79 GLU cc_start: 0.6888 (mp0) cc_final: 0.6512 (mp0) REVERT: E 89 GLN cc_start: 0.8827 (pp30) cc_final: 0.8246 (pp30) REVERT: E 90 GLN cc_start: 0.8085 (pp30) cc_final: 0.7845 (pp30) REVERT: E 137 ASN cc_start: 0.7844 (t0) cc_final: 0.7520 (t0) REVERT: F 11 LEU cc_start: 0.8121 (mt) cc_final: 0.7881 (mt) REVERT: F 25 SER cc_start: 0.8491 (m) cc_final: 0.7778 (p) REVERT: F 59 TYR cc_start: 0.8200 (m-80) cc_final: 0.7796 (m-80) REVERT: F 82 MET cc_start: 0.7242 (mpp) cc_final: 0.6601 (mpp) REVERT: F 106 TYR cc_start: 0.8063 (m-80) cc_final: 0.7736 (m-10) REVERT: F 124 SER cc_start: 0.7953 (m) cc_final: 0.7247 (p) REVERT: F 142 LEU cc_start: 0.7676 (pp) cc_final: 0.7346 (pp) REVERT: F 179 LEU cc_start: 0.7119 (mm) cc_final: 0.6682 (mt) REVERT: L 42 GLN cc_start: 0.7999 (mt0) cc_final: 0.7677 (mt0) REVERT: L 89 GLN cc_start: 0.8211 (tm130) cc_final: 0.7866 (tm130) REVERT: L 181 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7501 (pt) REVERT: R 4 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8563 (tt) REVERT: R 37 VAL cc_start: 0.8614 (p) cc_final: 0.8249 (m) REVERT: R 45 LEU cc_start: 0.8491 (mt) cc_final: 0.8215 (mp) REVERT: R 56 SER cc_start: 0.8611 (m) cc_final: 0.7868 (t) REVERT: R 63 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8397 (p) REVERT: R 149 TYR cc_start: 0.7765 (p90) cc_final: 0.6392 (p90) REVERT: R 163 LEU cc_start: 0.8180 (tp) cc_final: 0.7879 (tp) REVERT: R 179 LEU cc_start: 0.6604 (mm) cc_final: 0.6268 (mm) outliers start: 127 outliers final: 63 residues processed: 764 average time/residue: 1.2044 time to fit residues: 1114.0189 Evaluate side-chains 765 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 692 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 215 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 312 optimal weight: 4.9990 chunk 202 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 359 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 376 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 221 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 460 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN B 66 HIS B 354 ASN B 532 ASN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN C 207 HIS C 556 ASN C 613 GLN C 779 GLN C 787 GLN C 965 GLN E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.168249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130554 restraints weight = 77253.771| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.85 r_work: 0.3602 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31717 Z= 0.142 Angle : 0.617 11.872 43221 Z= 0.315 Chirality : 0.045 0.321 4985 Planarity : 0.005 0.072 5488 Dihedral : 5.210 57.753 5257 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.58 % Allowed : 17.15 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.13), residues: 3809 helix: 2.14 (0.19), residues: 724 sheet: 1.26 (0.15), residues: 1024 loop : -0.25 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 107 HIS 0.004 0.001 HIS B1058 PHE 0.029 0.001 PHE A 392 TYR 0.029 0.002 TYR R 33 ARG 0.018 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 17) link_NAG-ASN : angle 2.17916 ( 51) link_BETA1-4 : bond 0.00269 ( 15) link_BETA1-4 : angle 1.12358 ( 45) hydrogen bonds : bond 0.04531 ( 1313) hydrogen bonds : angle 5.61158 ( 3838) SS BOND : bond 0.00382 ( 45) SS BOND : angle 2.00603 ( 90) link_NAG-THR : bond 0.00500 ( 1) link_NAG-THR : angle 4.30191 ( 2) covalent geometry : bond 0.00325 (31639) covalent geometry : angle 0.60489 (43033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 705 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7984 (m-80) cc_final: 0.7772 (m-80) REVERT: A 108 THR cc_start: 0.8578 (m) cc_final: 0.8376 (m) REVERT: A 132 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 133 PHE cc_start: 0.8673 (m-80) cc_final: 0.7910 (m-80) REVERT: A 164 ASN cc_start: 0.8151 (t0) cc_final: 0.7748 (t0) REVERT: A 298 GLU cc_start: 0.8112 (tt0) cc_final: 0.7872 (tt0) REVERT: A 347 PHE cc_start: 0.8747 (m-80) cc_final: 0.8375 (m-80) REVERT: A 423 TYR cc_start: 0.7946 (t80) cc_final: 0.7574 (t80) REVERT: A 467 ASP cc_start: 0.7672 (t0) cc_final: 0.7418 (t0) REVERT: A 498 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7722 (mmm-85) REVERT: A 567 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: A 659 SER cc_start: 0.8469 (p) cc_final: 0.8269 (m) REVERT: A 718 PHE cc_start: 0.8775 (p90) cc_final: 0.8478 (p90) REVERT: A 740 MET cc_start: 0.8121 (mmm) cc_final: 0.7802 (tpt) REVERT: A 790 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8255 (mmmm) REVERT: A 825 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8330 (mttp) REVERT: A 950 ASP cc_start: 0.7779 (m-30) cc_final: 0.7469 (m-30) REVERT: A 1019 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7912 (tpt170) REVERT: A 1107 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7158 (mtt-85) REVERT: B 129 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7798 (mppt) REVERT: B 190 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: B 220 PHE cc_start: 0.8031 (t80) cc_final: 0.7802 (t80) REVERT: B 309 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7821 (mm-30) REVERT: B 347 PHE cc_start: 0.7529 (m-80) cc_final: 0.7105 (m-80) REVERT: B 349 SER cc_start: 0.8231 (m) cc_final: 0.7907 (p) REVERT: B 398 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6973 (p0) REVERT: B 410 ILE cc_start: 0.8995 (mm) cc_final: 0.8579 (pp) REVERT: B 495 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.6007 (t80) REVERT: B 505 HIS cc_start: 0.8071 (m-70) cc_final: 0.7788 (m-70) REVERT: B 508 TYR cc_start: 0.7573 (m-80) cc_final: 0.7372 (m-80) REVERT: B 773 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 904 TYR cc_start: 0.7648 (m-10) cc_final: 0.7416 (m-80) REVERT: B 950 ASP cc_start: 0.7615 (m-30) cc_final: 0.7251 (m-30) REVERT: B 990 GLU cc_start: 0.7613 (tt0) cc_final: 0.7064 (tm-30) REVERT: C 108 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7349 (t) REVERT: C 269 TYR cc_start: 0.8326 (m-80) cc_final: 0.7997 (m-80) REVERT: C 493 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7402 (mtp85) REVERT: C 516 GLU cc_start: 0.7676 (pp20) cc_final: 0.7211 (tm-30) REVERT: C 517 LEU cc_start: 0.8609 (mm) cc_final: 0.8078 (mt) REVERT: C 543 PHE cc_start: 0.8489 (m-10) cc_final: 0.8257 (m-10) REVERT: C 811 LYS cc_start: 0.8174 (mmpt) cc_final: 0.7876 (mptp) REVERT: C 900 MET cc_start: 0.8370 (mtp) cc_final: 0.8117 (mtt) REVERT: C 950 ASP cc_start: 0.7417 (m-30) cc_final: 0.7123 (m-30) REVERT: C 990 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 1045 LYS cc_start: 0.7777 (tptp) cc_final: 0.7196 (mmmt) REVERT: E 46 LEU cc_start: 0.8610 (tp) cc_final: 0.8355 (tp) REVERT: E 78 LEU cc_start: 0.7389 (mt) cc_final: 0.7017 (mt) REVERT: E 79 GLU cc_start: 0.6888 (mp0) cc_final: 0.6544 (mp0) REVERT: E 89 GLN cc_start: 0.8814 (pp30) cc_final: 0.8224 (pp30) REVERT: E 90 GLN cc_start: 0.7943 (pp30) cc_final: 0.7601 (pp30) REVERT: E 137 ASN cc_start: 0.7796 (t0) cc_final: 0.7482 (t0) REVERT: F 11 LEU cc_start: 0.8075 (mt) cc_final: 0.7860 (mt) REVERT: F 25 SER cc_start: 0.8456 (m) cc_final: 0.7758 (p) REVERT: F 59 TYR cc_start: 0.8204 (m-80) cc_final: 0.7841 (m-80) REVERT: F 82 MET cc_start: 0.7158 (mpp) cc_final: 0.6498 (mpp) REVERT: F 94 TYR cc_start: 0.8373 (m-80) cc_final: 0.7558 (m-80) REVERT: F 106 TYR cc_start: 0.8092 (m-80) cc_final: 0.7767 (m-10) REVERT: F 113 VAL cc_start: 0.9086 (p) cc_final: 0.8884 (m) REVERT: F 124 SER cc_start: 0.8067 (m) cc_final: 0.7333 (p) REVERT: F 142 LEU cc_start: 0.7660 (pp) cc_final: 0.7331 (pp) REVERT: F 179 LEU cc_start: 0.7110 (mm) cc_final: 0.6681 (mt) REVERT: L 11 LEU cc_start: 0.8294 (tp) cc_final: 0.7601 (mt) REVERT: L 42 GLN cc_start: 0.8018 (mt0) cc_final: 0.7704 (mt0) REVERT: L 89 GLN cc_start: 0.8197 (tm130) cc_final: 0.7912 (tm130) REVERT: L 181 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7375 (pt) REVERT: R 37 VAL cc_start: 0.8603 (p) cc_final: 0.8215 (m) REVERT: R 45 LEU cc_start: 0.8484 (mt) cc_final: 0.8214 (mp) REVERT: R 56 SER cc_start: 0.8352 (m) cc_final: 0.8043 (t) REVERT: R 63 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8419 (p) REVERT: R 103 TYR cc_start: 0.7881 (p90) cc_final: 0.7663 (p90) REVERT: R 149 TYR cc_start: 0.7775 (p90) cc_final: 0.6714 (p90) REVERT: R 163 LEU cc_start: 0.8202 (tp) cc_final: 0.7911 (tp) outliers start: 121 outliers final: 64 residues processed: 767 average time/residue: 1.1808 time to fit residues: 1106.0860 Evaluate side-chains 740 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 669 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 298 optimal weight: 0.0670 chunk 102 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 286 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 302 optimal weight: 0.0000 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN B 66 HIS B 532 ASN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 207 HIS C 556 ASN C 613 GLN C 703 ASN C 965 GLN C1134 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.169594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.133277 restraints weight = 59155.061| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.43 r_work: 0.3649 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31717 Z= 0.117 Angle : 0.610 11.920 43221 Z= 0.310 Chirality : 0.044 0.320 4985 Planarity : 0.004 0.075 5488 Dihedral : 4.973 51.590 5257 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.96 % Allowed : 18.31 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.13), residues: 3809 helix: 2.17 (0.19), residues: 728 sheet: 1.14 (0.15), residues: 1080 loop : -0.24 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 158 HIS 0.002 0.000 HIS C 66 PHE 0.031 0.001 PHE B 970 TYR 0.025 0.001 TYR B 170 ARG 0.017 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 17) link_NAG-ASN : angle 2.15818 ( 51) link_BETA1-4 : bond 0.00443 ( 15) link_BETA1-4 : angle 1.22603 ( 45) hydrogen bonds : bond 0.04088 ( 1313) hydrogen bonds : angle 5.46247 ( 3838) SS BOND : bond 0.00364 ( 45) SS BOND : angle 1.96574 ( 90) link_NAG-THR : bond 0.00563 ( 1) link_NAG-THR : angle 5.94138 ( 2) covalent geometry : bond 0.00260 (31639) covalent geometry : angle 0.59749 (43033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 697 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8222 (m-80) cc_final: 0.7921 (m-80) REVERT: A 133 PHE cc_start: 0.8464 (m-80) cc_final: 0.7612 (m-80) REVERT: A 164 ASN cc_start: 0.8181 (t0) cc_final: 0.7737 (t0) REVERT: A 191 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7158 (mt-10) REVERT: A 347 PHE cc_start: 0.8702 (m-80) cc_final: 0.8298 (m-80) REVERT: A 377 PHE cc_start: 0.8089 (t80) cc_final: 0.7739 (t80) REVERT: A 423 TYR cc_start: 0.7965 (t80) cc_final: 0.7623 (t80) REVERT: A 467 ASP cc_start: 0.7801 (t0) cc_final: 0.7533 (t0) REVERT: A 718 PHE cc_start: 0.8855 (p90) cc_final: 0.8570 (p90) REVERT: A 790 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8431 (mmmm) REVERT: A 825 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8415 (mttp) REVERT: A 950 ASP cc_start: 0.7937 (m-30) cc_final: 0.7635 (m-30) REVERT: A 1019 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8148 (tpt170) REVERT: A 1107 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7575 (mtt-85) REVERT: B 190 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7435 (mtp85) REVERT: B 220 PHE cc_start: 0.8008 (t80) cc_final: 0.7732 (t80) REVERT: B 309 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8092 (mm-30) REVERT: B 347 PHE cc_start: 0.7472 (m-80) cc_final: 0.6344 (m-80) REVERT: B 349 SER cc_start: 0.8136 (m) cc_final: 0.7773 (p) REVERT: B 398 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7133 (p0) REVERT: B 410 ILE cc_start: 0.9026 (mm) cc_final: 0.8608 (pp) REVERT: B 508 TYR cc_start: 0.7639 (m-80) cc_final: 0.7417 (m-80) REVERT: B 509 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7472 (mtt180) REVERT: B 773 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 904 TYR cc_start: 0.7954 (m-10) cc_final: 0.7679 (m-80) REVERT: B 990 GLU cc_start: 0.7744 (tt0) cc_final: 0.7071 (tm-30) REVERT: C 269 TYR cc_start: 0.8440 (m-80) cc_final: 0.8058 (m-80) REVERT: C 340 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7592 (pp20) REVERT: C 493 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7601 (mtp85) REVERT: C 516 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: C 517 LEU cc_start: 0.8571 (mm) cc_final: 0.8049 (mt) REVERT: C 811 LYS cc_start: 0.8249 (mmpt) cc_final: 0.7884 (mptp) REVERT: C 823 PHE cc_start: 0.8559 (t80) cc_final: 0.8354 (t80) REVERT: C 900 MET cc_start: 0.8516 (mtp) cc_final: 0.8291 (mtt) REVERT: C 950 ASP cc_start: 0.7591 (m-30) cc_final: 0.7286 (m-30) REVERT: C 1045 LYS cc_start: 0.7992 (tptp) cc_final: 0.7401 (mmpt) REVERT: E 11 LEU cc_start: 0.8235 (tp) cc_final: 0.7978 (tt) REVERT: E 46 LEU cc_start: 0.8658 (tp) cc_final: 0.8330 (tm) REVERT: E 79 GLU cc_start: 0.7039 (mp0) cc_final: 0.6665 (mp0) REVERT: E 89 GLN cc_start: 0.8856 (pp30) cc_final: 0.8272 (pp30) REVERT: E 90 GLN cc_start: 0.7962 (pp30) cc_final: 0.7669 (pp30) REVERT: E 129 THR cc_start: 0.7029 (m) cc_final: 0.6674 (p) REVERT: E 137 ASN cc_start: 0.7790 (t0) cc_final: 0.7426 (t0) REVERT: F 11 LEU cc_start: 0.8143 (mt) cc_final: 0.7902 (mt) REVERT: F 25 SER cc_start: 0.8453 (m) cc_final: 0.7791 (p) REVERT: F 59 TYR cc_start: 0.8320 (m-80) cc_final: 0.7878 (m-80) REVERT: F 106 TYR cc_start: 0.8174 (m-80) cc_final: 0.7860 (m-10) REVERT: F 113 VAL cc_start: 0.9100 (p) cc_final: 0.8896 (m) REVERT: F 124 SER cc_start: 0.8133 (m) cc_final: 0.7388 (p) REVERT: F 142 LEU cc_start: 0.7683 (pp) cc_final: 0.7354 (pp) REVERT: F 179 LEU cc_start: 0.7117 (mm) cc_final: 0.6697 (mt) REVERT: L 11 LEU cc_start: 0.8232 (tp) cc_final: 0.7557 (mt) REVERT: L 42 GLN cc_start: 0.7988 (mt0) cc_final: 0.7690 (mt0) REVERT: L 89 GLN cc_start: 0.8221 (tm130) cc_final: 0.7945 (tm130) REVERT: R 4 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8671 (tt) REVERT: R 37 VAL cc_start: 0.8601 (p) cc_final: 0.8263 (m) REVERT: R 45 LEU cc_start: 0.8528 (mt) cc_final: 0.8246 (mp) REVERT: R 56 SER cc_start: 0.8496 (m) cc_final: 0.8071 (t) REVERT: R 63 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8420 (p) REVERT: R 93 TYR cc_start: 0.8400 (m-80) cc_final: 0.8180 (m-80) REVERT: R 149 TYR cc_start: 0.7677 (p90) cc_final: 0.6553 (p90) REVERT: R 163 LEU cc_start: 0.8269 (tp) cc_final: 0.7978 (tp) REVERT: R 179 LEU cc_start: 0.6622 (mm) cc_final: 0.6301 (mm) outliers start: 100 outliers final: 54 residues processed: 740 average time/residue: 1.1640 time to fit residues: 1047.0433 Evaluate side-chains 735 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 676 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 141 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 375 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 474 GLN A 505 HIS A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN B 66 HIS ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 207 HIS C 556 ASN C 613 GLN C 616 ASN C 801 ASN C 955 ASN C1134 ASN E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.168765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131548 restraints weight = 67916.746| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.01 r_work: 0.3596 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 31717 Z= 0.148 Angle : 0.642 20.177 43221 Z= 0.326 Chirality : 0.045 0.312 4985 Planarity : 0.005 0.083 5488 Dihedral : 4.969 52.246 5257 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.11 % Allowed : 19.20 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.13), residues: 3809 helix: 2.08 (0.19), residues: 732 sheet: 1.19 (0.15), residues: 1048 loop : -0.27 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.004 0.001 HIS B1058 PHE 0.039 0.001 PHE A 392 TYR 0.028 0.002 TYR B1138 ARG 0.019 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 17) link_NAG-ASN : angle 2.16444 ( 51) link_BETA1-4 : bond 0.00244 ( 15) link_BETA1-4 : angle 1.14089 ( 45) hydrogen bonds : bond 0.04291 ( 1313) hydrogen bonds : angle 5.47901 ( 3838) SS BOND : bond 0.00407 ( 45) SS BOND : angle 2.46578 ( 90) link_NAG-THR : bond 0.00497 ( 1) link_NAG-THR : angle 5.37823 ( 2) covalent geometry : bond 0.00346 (31639) covalent geometry : angle 0.62667 (43033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 684 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.7790 (t0) cc_final: 0.7529 (t0) REVERT: A 191 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7312 (tt0) REVERT: A 420 ASP cc_start: 0.8527 (m-30) cc_final: 0.7781 (t0) REVERT: A 423 TYR cc_start: 0.7909 (t80) cc_final: 0.7585 (t80) REVERT: A 467 ASP cc_start: 0.7702 (t0) cc_final: 0.7438 (t0) REVERT: A 655 TYR cc_start: 0.8462 (t80) cc_final: 0.8136 (t80) REVERT: A 718 PHE cc_start: 0.8787 (p90) cc_final: 0.8478 (p90) REVERT: A 756 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6356 (t80) REVERT: A 790 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8267 (mmmm) REVERT: A 825 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8367 (mttm) REVERT: A 950 ASP cc_start: 0.7714 (m-30) cc_final: 0.7407 (m-30) REVERT: A 1019 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7943 (tpt170) REVERT: A 1107 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7292 (mtt-85) REVERT: B 220 PHE cc_start: 0.7993 (t80) cc_final: 0.7657 (t80) REVERT: B 309 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 347 PHE cc_start: 0.7460 (m-80) cc_final: 0.7011 (m-80) REVERT: B 349 SER cc_start: 0.8063 (m) cc_final: 0.7725 (p) REVERT: B 401 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8465 (t) REVERT: B 410 ILE cc_start: 0.8994 (mm) cc_final: 0.8552 (pp) REVERT: B 414 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8072 (mm110) REVERT: B 420 ASP cc_start: 0.8206 (p0) cc_final: 0.7958 (p0) REVERT: B 508 TYR cc_start: 0.7508 (m-80) cc_final: 0.7286 (m-10) REVERT: B 773 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7404 (tm-30) REVERT: B 821 LEU cc_start: 0.8693 (tp) cc_final: 0.8361 (tp) REVERT: B 825 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8199 (tppt) REVERT: B 904 TYR cc_start: 0.7832 (m-10) cc_final: 0.7485 (m-80) REVERT: B 947 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7945 (mtpt) REVERT: B 990 GLU cc_start: 0.7572 (tt0) cc_final: 0.6952 (tm-30) REVERT: C 269 TYR cc_start: 0.8329 (m-80) cc_final: 0.7963 (m-80) REVERT: C 441 LEU cc_start: 0.8594 (tp) cc_final: 0.8385 (tt) REVERT: C 442 ASP cc_start: 0.7498 (m-30) cc_final: 0.7298 (t0) REVERT: C 462 LYS cc_start: 0.8773 (mttp) cc_final: 0.8492 (mtpt) REVERT: C 493 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7420 (mtp85) REVERT: C 516 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: C 517 LEU cc_start: 0.8593 (mm) cc_final: 0.8083 (mt) REVERT: C 811 LYS cc_start: 0.8216 (mmpt) cc_final: 0.7879 (mptp) REVERT: C 823 PHE cc_start: 0.8444 (t80) cc_final: 0.8228 (t80) REVERT: C 900 MET cc_start: 0.8455 (mtp) cc_final: 0.8189 (mtt) REVERT: C 950 ASP cc_start: 0.7393 (m-30) cc_final: 0.7082 (m-30) REVERT: C 1045 LYS cc_start: 0.7798 (tptp) cc_final: 0.7272 (mmmt) REVERT: E 11 LEU cc_start: 0.8224 (tp) cc_final: 0.7951 (tt) REVERT: E 46 LEU cc_start: 0.8603 (tp) cc_final: 0.8293 (tm) REVERT: E 79 GLU cc_start: 0.6888 (mp0) cc_final: 0.6446 (mp0) REVERT: E 82 ASP cc_start: 0.8391 (m-30) cc_final: 0.7798 (m-30) REVERT: E 85 VAL cc_start: 0.7931 (t) cc_final: 0.7537 (p) REVERT: E 89 GLN cc_start: 0.8813 (pp30) cc_final: 0.8168 (pp30) REVERT: E 90 GLN cc_start: 0.7838 (pp30) cc_final: 0.7546 (pp30) REVERT: E 129 THR cc_start: 0.6985 (m) cc_final: 0.6717 (p) REVERT: F 11 LEU cc_start: 0.8102 (mt) cc_final: 0.7848 (mt) REVERT: F 25 SER cc_start: 0.8399 (m) cc_final: 0.7720 (p) REVERT: F 33 TYR cc_start: 0.8012 (m-10) cc_final: 0.7598 (m-80) REVERT: F 59 TYR cc_start: 0.8217 (m-80) cc_final: 0.7774 (m-80) REVERT: F 94 TYR cc_start: 0.8322 (m-80) cc_final: 0.7538 (m-80) REVERT: F 106 TYR cc_start: 0.8088 (m-80) cc_final: 0.7760 (m-10) REVERT: F 124 SER cc_start: 0.8016 (m) cc_final: 0.7221 (p) REVERT: F 142 LEU cc_start: 0.7654 (pp) cc_final: 0.7320 (pp) REVERT: F 179 LEU cc_start: 0.7116 (mm) cc_final: 0.6678 (mt) REVERT: L 11 LEU cc_start: 0.8228 (tp) cc_final: 0.7540 (mt) REVERT: L 42 GLN cc_start: 0.7955 (mt0) cc_final: 0.7632 (mt0) REVERT: L 89 GLN cc_start: 0.8197 (tm130) cc_final: 0.7878 (tm130) REVERT: L 181 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7316 (pt) REVERT: R 4 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8581 (tt) REVERT: R 20 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8197 (mm) REVERT: R 37 VAL cc_start: 0.8528 (p) cc_final: 0.8206 (m) REVERT: R 45 LEU cc_start: 0.8511 (mt) cc_final: 0.8229 (mp) REVERT: R 56 SER cc_start: 0.8389 (m) cc_final: 0.7932 (t) REVERT: R 63 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8364 (p) REVERT: R 80 LEU cc_start: 0.8019 (tt) cc_final: 0.7763 (tt) REVERT: R 93 TYR cc_start: 0.8397 (m-80) cc_final: 0.8115 (m-80) REVERT: R 149 TYR cc_start: 0.7671 (p90) cc_final: 0.6566 (p90) REVERT: R 163 LEU cc_start: 0.8207 (tp) cc_final: 0.7911 (tp) REVERT: R 179 LEU cc_start: 0.6734 (mm) cc_final: 0.6454 (mm) outliers start: 105 outliers final: 63 residues processed: 732 average time/residue: 1.2197 time to fit residues: 1089.2317 Evaluate side-chains 741 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 670 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 69 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 289 optimal weight: 0.6980 chunk 358 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 227 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 474 GLN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1074 ASN B 66 HIS ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN C 207 HIS C 556 ASN C 613 GLN C 703 ASN C 949 GLN C 955 ASN C1005 GLN C1134 ASN E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.167745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.131616 restraints weight = 56068.772| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.38 r_work: 0.3628 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31717 Z= 0.185 Angle : 0.659 16.773 43221 Z= 0.336 Chirality : 0.046 0.309 4985 Planarity : 0.005 0.090 5488 Dihedral : 5.007 52.357 5257 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.02 % Allowed : 19.52 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 3809 helix: 1.99 (0.19), residues: 731 sheet: 1.16 (0.15), residues: 1039 loop : -0.33 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS B1058 PHE 0.043 0.002 PHE A 392 TYR 0.030 0.002 TYR C 453 ARG 0.020 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 17) link_NAG-ASN : angle 2.20725 ( 51) link_BETA1-4 : bond 0.00272 ( 15) link_BETA1-4 : angle 1.10282 ( 45) hydrogen bonds : bond 0.04554 ( 1313) hydrogen bonds : angle 5.52522 ( 3838) SS BOND : bond 0.00422 ( 45) SS BOND : angle 2.35216 ( 90) link_NAG-THR : bond 0.00599 ( 1) link_NAG-THR : angle 5.74316 ( 2) covalent geometry : bond 0.00431 (31639) covalent geometry : angle 0.64514 (43033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 670 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.7875 (t0) cc_final: 0.7613 (t0) REVERT: A 191 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7552 (tt0) REVERT: A 420 ASP cc_start: 0.8428 (m-30) cc_final: 0.7816 (t0) REVERT: A 423 TYR cc_start: 0.7964 (t80) cc_final: 0.7717 (t80) REVERT: A 467 ASP cc_start: 0.7818 (t0) cc_final: 0.7576 (t0) REVERT: A 490 PHE cc_start: 0.7832 (t80) cc_final: 0.7341 (t80) REVERT: A 718 PHE cc_start: 0.8917 (p90) cc_final: 0.8579 (p90) REVERT: A 756 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6489 (t80) REVERT: A 790 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8438 (mmmm) REVERT: A 825 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8422 (mttp) REVERT: A 950 ASP cc_start: 0.8093 (m-30) cc_final: 0.7780 (m-30) REVERT: A 1019 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8145 (tpt170) REVERT: B 129 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7987 (mppt) REVERT: B 190 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7621 (mtp85) REVERT: B 220 PHE cc_start: 0.8031 (t80) cc_final: 0.7675 (t80) REVERT: B 309 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8100 (mm-30) REVERT: B 347 PHE cc_start: 0.7647 (m-80) cc_final: 0.7163 (m-80) REVERT: B 349 SER cc_start: 0.8137 (m) cc_final: 0.7791 (p) REVERT: B 398 ASP cc_start: 0.7546 (p0) cc_final: 0.7179 (p0) REVERT: B 401 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8489 (t) REVERT: B 410 ILE cc_start: 0.9028 (mm) cc_final: 0.8804 (tp) REVERT: B 508 TYR cc_start: 0.7557 (m-80) cc_final: 0.7351 (m-10) REVERT: B 773 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 950 ASP cc_start: 0.7922 (m-30) cc_final: 0.7665 (m-30) REVERT: B 990 GLU cc_start: 0.7819 (tt0) cc_final: 0.7131 (tm-30) REVERT: C 269 TYR cc_start: 0.8482 (m-80) cc_final: 0.8162 (m-80) REVERT: C 340 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7661 (pp20) REVERT: C 442 ASP cc_start: 0.7683 (m-30) cc_final: 0.7346 (t0) REVERT: C 462 LYS cc_start: 0.8908 (mttp) cc_final: 0.8595 (mtpt) REVERT: C 493 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7609 (mtp85) REVERT: C 516 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: C 517 LEU cc_start: 0.8600 (mm) cc_final: 0.8092 (mt) REVERT: C 574 ASP cc_start: 0.8034 (t0) cc_final: 0.7710 (p0) REVERT: C 811 LYS cc_start: 0.8301 (mmpt) cc_final: 0.7952 (mptp) REVERT: C 823 PHE cc_start: 0.8575 (t80) cc_final: 0.8258 (t80) REVERT: C 900 MET cc_start: 0.8566 (mtp) cc_final: 0.8317 (mtt) REVERT: C 1045 LYS cc_start: 0.7965 (tptp) cc_final: 0.7391 (mmmt) REVERT: E 11 LEU cc_start: 0.8245 (tp) cc_final: 0.7989 (tt) REVERT: E 46 LEU cc_start: 0.8681 (tp) cc_final: 0.8388 (tm) REVERT: E 79 GLU cc_start: 0.7039 (mp0) cc_final: 0.6563 (mp0) REVERT: E 82 ASP cc_start: 0.8494 (m-30) cc_final: 0.7903 (m-30) REVERT: E 89 GLN cc_start: 0.8820 (pp30) cc_final: 0.8203 (pp30) REVERT: E 90 GLN cc_start: 0.7960 (pp30) cc_final: 0.7621 (pp30) REVERT: E 129 THR cc_start: 0.7139 (m) cc_final: 0.6796 (p) REVERT: E 137 ASN cc_start: 0.7775 (t0) cc_final: 0.7450 (t0) REVERT: F 11 LEU cc_start: 0.8138 (mt) cc_final: 0.7900 (mt) REVERT: F 25 SER cc_start: 0.8434 (m) cc_final: 0.7763 (p) REVERT: F 33 TYR cc_start: 0.8088 (m-10) cc_final: 0.7653 (m-80) REVERT: F 59 TYR cc_start: 0.8333 (m-80) cc_final: 0.7963 (m-80) REVERT: F 94 TYR cc_start: 0.8381 (m-80) cc_final: 0.7610 (m-80) REVERT: F 106 TYR cc_start: 0.8200 (m-80) cc_final: 0.7935 (m-10) REVERT: F 124 SER cc_start: 0.8227 (m) cc_final: 0.7452 (p) REVERT: F 142 LEU cc_start: 0.7671 (pp) cc_final: 0.7336 (pp) REVERT: F 179 LEU cc_start: 0.7249 (mm) cc_final: 0.6793 (mt) REVERT: L 11 LEU cc_start: 0.8227 (tp) cc_final: 0.7548 (mt) REVERT: L 42 GLN cc_start: 0.8010 (mt0) cc_final: 0.7707 (mt0) REVERT: L 89 GLN cc_start: 0.8280 (tm130) cc_final: 0.8039 (tm130) REVERT: L 181 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7342 (pt) REVERT: R 4 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8662 (tt) REVERT: R 37 VAL cc_start: 0.8599 (p) cc_final: 0.8267 (m) REVERT: R 45 LEU cc_start: 0.8555 (mt) cc_final: 0.8277 (mp) REVERT: R 56 SER cc_start: 0.8514 (m) cc_final: 0.8059 (t) REVERT: R 63 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8410 (p) REVERT: R 80 LEU cc_start: 0.8135 (tt) cc_final: 0.7934 (tt) REVERT: R 93 TYR cc_start: 0.8510 (m-80) cc_final: 0.8253 (m-80) REVERT: R 149 TYR cc_start: 0.7746 (p90) cc_final: 0.6679 (p90) REVERT: R 163 LEU cc_start: 0.8293 (tp) cc_final: 0.8004 (tp) REVERT: R 179 LEU cc_start: 0.6814 (mm) cc_final: 0.6526 (mm) outliers start: 102 outliers final: 67 residues processed: 719 average time/residue: 1.6065 time to fit residues: 1454.2721 Evaluate side-chains 738 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 665 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 165 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 218 optimal weight: 0.0980 chunk 278 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 354 optimal weight: 0.4980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1074 ASN B 30 ASN B 66 HIS B 474 GLN C 207 HIS C 556 ASN C 613 GLN C 949 GLN C 955 ASN C1134 ASN E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.167416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130646 restraints weight = 71623.144| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.93 r_work: 0.3586 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31717 Z= 0.170 Angle : 0.665 14.023 43221 Z= 0.339 Chirality : 0.045 0.308 4985 Planarity : 0.005 0.089 5488 Dihedral : 5.017 52.228 5257 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 20.05 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 3809 helix: 1.99 (0.19), residues: 730 sheet: 1.12 (0.15), residues: 1057 loop : -0.37 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.005 0.001 HIS B1058 PHE 0.037 0.002 PHE A 392 TYR 0.032 0.002 TYR C 904 ARG 0.022 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 17) link_NAG-ASN : angle 2.18696 ( 51) link_BETA1-4 : bond 0.00272 ( 15) link_BETA1-4 : angle 1.10349 ( 45) hydrogen bonds : bond 0.04501 ( 1313) hydrogen bonds : angle 5.52694 ( 3838) SS BOND : bond 0.00403 ( 45) SS BOND : angle 2.18808 ( 90) link_NAG-THR : bond 0.00547 ( 1) link_NAG-THR : angle 6.07886 ( 2) covalent geometry : bond 0.00395 (31639) covalent geometry : angle 0.65219 (43033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7618 Ramachandran restraints generated. 3809 Oldfield, 0 Emsley, 3809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 676 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.7647 (t0) cc_final: 0.7405 (t0) REVERT: A 191 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7067 (tt0) REVERT: A 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.7938 (t0) REVERT: A 423 TYR cc_start: 0.7899 (t80) cc_final: 0.7660 (t80) REVERT: A 467 ASP cc_start: 0.7693 (t0) cc_final: 0.7462 (t0) REVERT: A 474 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8355 (tp40) REVERT: A 490 PHE cc_start: 0.7728 (t80) cc_final: 0.7257 (t80) REVERT: A 655 TYR cc_start: 0.8449 (t80) cc_final: 0.8150 (t80) REVERT: A 718 PHE cc_start: 0.8857 (p90) cc_final: 0.8532 (p90) REVERT: A 756 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6305 (t80) REVERT: A 790 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8285 (mmmm) REVERT: A 825 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8305 (mttp) REVERT: A 950 ASP cc_start: 0.7812 (m-30) cc_final: 0.7502 (m-30) REVERT: A 1019 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7899 (tpt170) REVERT: A 1107 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7189 (mtm-85) REVERT: A 1128 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8783 (t) REVERT: B 33 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8178 (p) REVERT: B 127 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7774 (m) REVERT: B 190 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7500 (mtp85) REVERT: B 220 PHE cc_start: 0.8005 (t80) cc_final: 0.7687 (t80) REVERT: B 347 PHE cc_start: 0.7637 (m-80) cc_final: 0.7162 (m-80) REVERT: B 349 SER cc_start: 0.8136 (m) cc_final: 0.7785 (p) REVERT: B 398 ASP cc_start: 0.7465 (p0) cc_final: 0.7113 (p0) REVERT: B 401 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8451 (t) REVERT: B 410 ILE cc_start: 0.9013 (mm) cc_final: 0.8765 (tp) REVERT: B 489 TYR cc_start: 0.8076 (m-80) cc_final: 0.7773 (m-10) REVERT: B 904 TYR cc_start: 0.7700 (m-10) cc_final: 0.7490 (m-80) REVERT: B 969 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8389 (mtpt) REVERT: B 990 GLU cc_start: 0.7604 (tt0) cc_final: 0.6996 (tm-30) REVERT: C 235 ILE cc_start: 0.8606 (mt) cc_final: 0.8355 (tt) REVERT: C 239 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 269 TYR cc_start: 0.8345 (m-80) cc_final: 0.8060 (m-80) REVERT: C 340 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7425 (pp20) REVERT: C 442 ASP cc_start: 0.7447 (m-30) cc_final: 0.7244 (t0) REVERT: C 493 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7405 (mtp85) REVERT: C 516 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: C 517 LEU cc_start: 0.8605 (mm) cc_final: 0.8131 (mt) REVERT: C 811 LYS cc_start: 0.8269 (mmpt) cc_final: 0.7952 (mptp) REVERT: C 823 PHE cc_start: 0.8439 (t80) cc_final: 0.8201 (t80) REVERT: C 900 MET cc_start: 0.8401 (mtp) cc_final: 0.8189 (mtt) REVERT: C 904 TYR cc_start: 0.7682 (m-10) cc_final: 0.7382 (m-10) REVERT: C 950 ASP cc_start: 0.7267 (m-30) cc_final: 0.7022 (m-30) REVERT: C 979 ASP cc_start: 0.7615 (t0) cc_final: 0.7113 (t0) REVERT: C 1045 LYS cc_start: 0.7763 (tptp) cc_final: 0.7157 (mmmt) REVERT: E 11 LEU cc_start: 0.8210 (tp) cc_final: 0.7940 (tt) REVERT: E 46 LEU cc_start: 0.8622 (tp) cc_final: 0.8329 (tm) REVERT: E 79 GLU cc_start: 0.6908 (mp0) cc_final: 0.6444 (mp0) REVERT: E 82 ASP cc_start: 0.8433 (m-30) cc_final: 0.7883 (m-30) REVERT: E 89 GLN cc_start: 0.8778 (pp30) cc_final: 0.8142 (pp30) REVERT: E 90 GLN cc_start: 0.7918 (pp30) cc_final: 0.7595 (pp30) REVERT: E 129 THR cc_start: 0.7106 (m) cc_final: 0.6813 (p) REVERT: F 11 LEU cc_start: 0.8082 (mt) cc_final: 0.7849 (mt) REVERT: F 25 SER cc_start: 0.8390 (m) cc_final: 0.7720 (p) REVERT: F 33 TYR cc_start: 0.8014 (m-10) cc_final: 0.7647 (m-80) REVERT: F 59 TYR cc_start: 0.8251 (m-80) cc_final: 0.7888 (m-80) REVERT: F 81 GLN cc_start: 0.8593 (tp40) cc_final: 0.8276 (tp40) REVERT: F 94 TYR cc_start: 0.8323 (m-80) cc_final: 0.7595 (m-80) REVERT: F 106 TYR cc_start: 0.8091 (m-80) cc_final: 0.7826 (m-10) REVERT: F 124 SER cc_start: 0.8115 (m) cc_final: 0.7314 (p) REVERT: F 142 LEU cc_start: 0.7631 (pp) cc_final: 0.7287 (pp) REVERT: F 179 LEU cc_start: 0.7265 (mm) cc_final: 0.6814 (mt) REVERT: L 11 LEU cc_start: 0.8222 (tp) cc_final: 0.7541 (mt) REVERT: L 42 GLN cc_start: 0.8000 (mt0) cc_final: 0.7683 (mt0) REVERT: L 89 GLN cc_start: 0.8241 (tm130) cc_final: 0.7920 (tm130) REVERT: L 181 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (pt) REVERT: R 4 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8666 (tt) REVERT: R 37 VAL cc_start: 0.8569 (p) cc_final: 0.8254 (m) REVERT: R 45 LEU cc_start: 0.8526 (mt) cc_final: 0.8254 (mp) REVERT: R 56 SER cc_start: 0.8451 (m) cc_final: 0.7987 (t) REVERT: R 63 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8366 (p) REVERT: R 80 LEU cc_start: 0.8096 (tt) cc_final: 0.7893 (tt) REVERT: R 149 TYR cc_start: 0.7712 (p90) cc_final: 0.6694 (p90) REVERT: R 163 LEU cc_start: 0.8227 (tp) cc_final: 0.7932 (tp) REVERT: R 179 LEU cc_start: 0.6793 (mm) cc_final: 0.6501 (mm) outliers start: 88 outliers final: 66 residues processed: 718 average time/residue: 1.2022 time to fit residues: 1046.7247 Evaluate side-chains 746 residues out of total 3377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 670 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 367 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 305 optimal weight: 0.0870 chunk 210 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 185 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1074 ASN B 30 ASN B 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN C 207 HIS C 556 ASN C 613 GLN C1134 ASN E 37 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.167731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131094 restraints weight = 67510.913| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.92 r_work: 0.3590 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31717 Z= 0.157 Angle : 0.661 12.811 43221 Z= 0.338 Chirality : 0.045 0.307 4985 Planarity : 0.005 0.090 5488 Dihedral : 5.007 52.338 5257 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.66 % Allowed : 20.32 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 3809 helix: 1.93 (0.19), residues: 736 sheet: 1.07 (0.15), residues: 1054 loop : -0.36 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS B1058 PHE 0.038 0.001 PHE A 392 TYR 0.030 0.002 TYR C 453 ARG 0.022 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 17) link_NAG-ASN : angle 2.18145 ( 51) link_BETA1-4 : bond 0.00258 ( 15) link_BETA1-4 : angle 1.10865 ( 45) hydrogen bonds : bond 0.04428 ( 1313) hydrogen bonds : angle 5.49355 ( 3838) SS BOND : bond 0.00420 ( 45) SS BOND : angle 2.31566 ( 90) link_NAG-THR : bond 0.00565 ( 1) link_NAG-THR : angle 6.18576 ( 2) covalent geometry : bond 0.00365 (31639) covalent geometry : angle 0.64713 (43033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36246.21 seconds wall clock time: 619 minutes 46.63 seconds (37186.63 seconds total)