Starting phenix.real_space_refine on Thu Jun 19 16:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wly_37635/06_2025/8wly_37635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wly_37635/06_2025/8wly_37635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wly_37635/06_2025/8wly_37635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wly_37635/06_2025/8wly_37635.map" model { file = "/net/cci-nas-00/data/ceres_data/8wly_37635/06_2025/8wly_37635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wly_37635/06_2025/8wly_37635_neut.cif" } resolution = 3.96 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= 0.000 sd= 0.002 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 107 5.16 5 C 14353 2.51 5 N 3694 2.21 5 O 4444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22598 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6757 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 46, 'TRANS': 823} Chain breaks: 4 Chain: "B" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8325 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 60, 'TRANS': 1006} Chain breaks: 2 Chain: "C" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6769 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 46, 'TRANS': 824} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.24, per 1000 atoms: 0.59 Number of scatterers: 22598 At special positions: 0 Unit cell: (162.204, 145.017, 151.462, 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 107 16.00 O 4444 8.00 N 3694 7.00 C 14353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.04 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.02 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.04 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.06 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.02 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.05 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.02 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 270 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 692 " " NAG A1304 " - " ASN A1057 " " NAG B1301 " - " ASN B 66 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 692 " " NAG B1304 " - " ASN B1057 " " NAG B1305 " - " ASN B1117 " " NAG B1306 " - " ASN B 319 " " NAG C1301 " - " ASN C 66 " " NAG C1302 " - " ASN C 110 " " NAG C1303 " - " ASN C 159 " " NAG C1304 " - " ASN C 228 " " NAG C1305 " - " ASN C 590 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 692 " " NAG C1308 " - " ASN C1057 " " NAG C1309 " - " ASN C 120 " " NAG D 1 " - " ASN A 700 " " NAG E 1 " - " ASN A1081 " " NAG F 1 " - " ASN A1117 " " NAG G 1 " - " ASN A 784 " " NAG H 1 " - " ASN B 120 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 590 " " NAG K 1 " - " ASN B 700 " " NAG L 1 " - " ASN B 784 " " NAG M 1 " - " ASN B1081 " " NAG N 1 " - " ASN B 270 " " NAG O 1 " - " ASN C 270 " " NAG P 1 " - " ASN C 700 " " NAG Q 1 " - " ASN C 784 " " NAG R 1 " - " ASN C1081 " " NAG S 1 " - " ASN C1117 " Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 3.0 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 42 sheets defined 23.5% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.530A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 741 through 766 removed outlier: 3.561A pdb=" N GLN A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.521A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 868 Processing helix chain 'A' and resid 880 through 892 removed outlier: 3.561A pdb=" N ILE A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 923 removed outlier: 4.017A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 904 " --> pdb=" O TYR A 900 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.891A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 968 through 1015 removed outlier: 3.781A pdb=" N VAL A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 352 through 360 removed outlier: 4.181A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.691A pdb=" N LEU B 375 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 396 removed outlier: 4.529A pdb=" N ARG B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 392 through 396' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 741 through 766 Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.024A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 950 Processing helix chain 'B' and resid 959 through 967 Processing helix chain 'B' and resid 968 through 1016 removed outlier: 4.425A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 741 through 766 removed outlier: 3.604A pdb=" N THR C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 810 removed outlier: 3.655A pdb=" N THR C 810 " --> pdb=" O PHE C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 867 removed outlier: 3.560A pdb=" N TYR C 856 " --> pdb=" O MET C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.818A pdb=" N PHE C 871 " --> pdb=" O GLY C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 893 Processing helix chain 'C' and resid 895 through 902 removed outlier: 4.428A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 900 " --> pdb=" O GLN C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 removed outlier: 3.590A pdb=" N VAL C 934 " --> pdb=" O LYS C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 967 Processing helix chain 'C' and resid 968 through 1016 removed outlier: 4.380A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.047A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 67 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR A 72 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 251 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 88 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 182 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 221 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER A 199 " --> pdb=" O PRO A 219 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N TYR A 201 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 217 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.824A pdb=" N PHE A 48 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY C 553 " --> pdb=" O ASP C 561 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS C 312 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASN C 529 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 314 " --> pdb=" O ASN C 529 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 60 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.927A pdb=" N GLY A 101 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 237 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 99 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A 102 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 118 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 125 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 530 removed outlier: 4.914A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 553 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE A 552 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 630 through 631 Processing sheet with id=AA9, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.407A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA A 659 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.070A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.523A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A1038 " --> pdb=" O GLY A1042 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A1044 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A1046 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A1034 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1048 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.709A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.871A pdb=" N SER C 686 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB6, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB7, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.668A pdb=" N THR B 32 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER B 199 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N TYR B 201 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU B 217 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ASN B 215 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 39 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N LEU B 217 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 60 removed outlier: 3.842A pdb=" N ASP B 275 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.346A pdb=" N PHE B 139 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 140 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.924A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 237 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 99 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER B 112 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B 131 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU B 124 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 299 through 306 removed outlier: 3.521A pdb=" N THR B 586 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 582 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 305 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 580 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 346 removed outlier: 5.269A pdb=" N ASN B 382 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 503 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 342 through 346 Processing sheet with id=AC6, first strand: chain 'B' and resid 441 through 442 Processing sheet with id=AC7, first strand: chain 'B' and resid 526 through 530 removed outlier: 3.544A pdb=" N PHE B 530 " --> pdb=" O LEU B 533 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.197A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 659 " --> pdb=" O PRO B 652 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 684 through 686 Processing sheet with id=AD1, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.463A pdb=" N GLN B1054 " --> pdb=" O THR B 699 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 701 " --> pdb=" O PRO B1052 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 703 " --> pdb=" O TYR B1050 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR B1050 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 705 " --> pdb=" O VAL B1048 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B1048 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR B 707 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B1046 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 709 " --> pdb=" O VAL B1044 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1044 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY B1042 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B1033 " --> pdb=" O VAL B1048 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AD4, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.059A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 35 removed outlier: 4.050A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 253 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 57 removed outlier: 4.119A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 148 through 149 removed outlier: 4.308A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR C 237 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE C 99 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU C 124 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN C 130 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N CYS C 160 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLU C 132 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N PHE C 158 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AE1, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.557A pdb=" N ALA C 659 " --> pdb=" O PRO C 652 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.929A pdb=" N GLN C1054 " --> pdb=" O THR C 699 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 701 " --> pdb=" O PRO C1052 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 703 " --> pdb=" O TYR C1050 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C1050 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 705 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1048 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 707 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C1046 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 709 " --> pdb=" O VAL C1044 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C1044 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1042 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C1033 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.929A pdb=" N GLN C1054 " --> pdb=" O THR C 699 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 701 " --> pdb=" O PRO C1052 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 703 " --> pdb=" O TYR C1050 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C1050 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 705 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1048 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 707 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C1046 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 709 " --> pdb=" O VAL C1044 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C1044 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1042 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C1059 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C1096 " --> pdb=" O ILE C1087 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AE5, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AE6, first strand: chain 'C' and resid 1103 through 1104 removed outlier: 3.519A pdb=" N ILE C1064 " --> pdb=" O TYR C1071 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2451 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: 10.01 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5662 1.33 - 1.46: 5363 1.46 - 1.58: 11931 1.58 - 1.70: 0 1.70 - 1.83: 146 Bond restraints: 23102 Sorted by residual: bond pdb=" CA PRO C 969 " pdb=" C PRO C 969 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.74e+01 bond pdb=" C THR C 540 " pdb=" O THR C 540 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.01e-02 9.80e+03 9.14e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C SER B 575 " pdb=" N PRO B 576 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.25e-02 6.40e+03 7.68e+00 bond pdb=" C THR C 540 " pdb=" N PRO C 541 " ideal model delta sigma weight residual 1.332 1.364 -0.033 1.32e-02 5.74e+03 6.06e+00 ... (remaining 23097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 31113 3.12 - 6.24: 273 6.24 - 9.36: 33 9.36 - 12.48: 8 12.48 - 15.60: 1 Bond angle restraints: 31428 Sorted by residual: angle pdb=" N ASN B 734 " pdb=" CA ASN B 734 " pdb=" C ASN B 734 " ideal model delta sigma weight residual 111.36 100.94 10.42 1.09e+00 8.42e-01 9.13e+01 angle pdb=" N SER B 578 " pdb=" CA SER B 578 " pdb=" C SER B 578 " ideal model delta sigma weight residual 111.39 123.79 -12.40 1.38e+00 5.25e-01 8.08e+01 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 108.54 96.21 12.33 1.41e+00 5.03e-01 7.64e+01 angle pdb=" N GLY C 740 " pdb=" CA GLY C 740 " pdb=" C GLY C 740 " ideal model delta sigma weight residual 111.36 121.35 -9.99 1.17e+00 7.31e-01 7.29e+01 angle pdb=" N TYR B 724 " pdb=" CA TYR B 724 " pdb=" C TYR B 724 " ideal model delta sigma weight residual 112.12 101.06 11.06 1.34e+00 5.57e-01 6.81e+01 ... (remaining 31423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 13152 21.31 - 42.61: 1122 42.61 - 63.92: 199 63.92 - 85.22: 36 85.22 - 106.53: 20 Dihedral angle restraints: 14529 sinusoidal: 6363 harmonic: 8166 Sorted by residual: dihedral pdb=" CB CYS B 20 " pdb=" SG CYS B 20 " pdb=" SG CYS B 134 " pdb=" CB CYS B 134 " ideal model delta sinusoidal sigma weight residual -86.00 -158.94 72.94 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" SG CYS B 577 " pdb=" CB CYS B 577 " ideal model delta sinusoidal sigma weight residual 93.00 24.05 68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS C 20 " pdb=" SG CYS C 20 " pdb=" SG CYS C 134 " pdb=" CB CYS C 134 " ideal model delta sinusoidal sigma weight residual -86.00 -136.09 50.09 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 14526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3638 0.136 - 0.271: 71 0.271 - 0.407: 10 0.407 - 0.542: 2 0.542 - 0.678: 3 Chirality restraints: 3724 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 692 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 3721 not shown) Planarity restraints: 4059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 968 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" CG ASP B 968 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP B 968 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP B 968 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 242 " -0.044 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO B 243 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1125 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO C1126 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C1126 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1126 " -0.036 5.00e-02 4.00e+02 ... (remaining 4056 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2428 2.75 - 3.28: 22627 3.28 - 3.82: 37587 3.82 - 4.36: 44709 4.36 - 4.90: 75284 Nonbonded interactions: 182635 Sorted by model distance: nonbonded pdb=" O GLN A 918 " pdb=" OG1 THR A 922 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 293 " pdb=" O GLU A 295 " model vdw 2.214 3.040 nonbonded pdb=" OG SER C 718 " pdb=" OG1 THR C 842 " model vdw 2.219 3.040 nonbonded pdb=" O PHE A 552 " pdb=" N PHE B 48 " model vdw 2.250 3.120 nonbonded pdb=" OG SER C 36 " pdb=" O SER C 65 " model vdw 2.251 3.040 ... (remaining 182630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 19 through 598 or resid 600 through 1127 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.700 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.005 0.057 23190 Z= 0.253 Angle : 0.886 16.701 31658 Z= 0.501 Chirality : 0.058 0.678 3724 Planarity : 0.005 0.068 4024 Dihedral : 15.955 106.526 9155 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 1.06 % Allowed : 20.53 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.15), residues: 2784 helix: 1.92 (0.21), residues: 586 sheet: -0.13 (0.21), residues: 538 loop : -1.38 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 246 HIS 0.007 0.001 HIS C 54 PHE 0.023 0.002 PHE B 77 TYR 0.024 0.002 TYR A 887 ARG 0.005 0.001 ARG B 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 35) link_NAG-ASN : angle 3.95107 ( 105) link_BETA1-4 : bond 0.00663 ( 19) link_BETA1-4 : angle 1.92726 ( 57) hydrogen bonds : bond 0.15967 ( 868) hydrogen bonds : angle 7.43268 ( 2451) SS BOND : bond 0.00703 ( 34) SS BOND : angle 1.38698 ( 68) covalent geometry : bond 0.00468 (23102) covalent geometry : angle 0.85305 (31428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 450 ARG cc_start: 0.8261 (mtm180) cc_final: 0.8035 (mtm180) REVERT: C 106 SER cc_start: 0.4163 (OUTLIER) cc_final: 0.3603 (t) REVERT: C 108 MET cc_start: 0.3777 (OUTLIER) cc_final: 0.2039 (ttm) REVERT: C 723 MET cc_start: 0.8015 (mmm) cc_final: 0.7795 (mmm) REVERT: C 747 ASN cc_start: 0.8019 (m110) cc_final: 0.7723 (t0) outliers start: 26 outliers final: 5 residues processed: 222 average time/residue: 0.3279 time to fit residues: 115.8831 Evaluate side-chains 152 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 221 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 163 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 136 ASN B 148 GLN B 747 ASN B 940 GLN C 54 HIS C 631 GLN C 745 GLN C 747 ASN ** C 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN C1006 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.109587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084010 restraints weight = 70813.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083396 restraints weight = 60068.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084186 restraints weight = 46884.797| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23190 Z= 0.142 Angle : 0.670 14.513 31658 Z= 0.335 Chirality : 0.048 0.538 3724 Planarity : 0.005 0.062 4024 Dihedral : 8.168 61.184 4135 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 2.69 % Allowed : 20.29 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.15), residues: 2784 helix: 2.06 (0.21), residues: 601 sheet: -0.09 (0.21), residues: 529 loop : -1.31 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 246 HIS 0.005 0.001 HIS B 642 PHE 0.017 0.001 PHE B 330 TYR 0.017 0.001 TYR A 253 ARG 0.004 0.001 ARG A1002 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 35) link_NAG-ASN : angle 3.44051 ( 105) link_BETA1-4 : bond 0.00430 ( 19) link_BETA1-4 : angle 1.70226 ( 57) hydrogen bonds : bond 0.05276 ( 868) hydrogen bonds : angle 6.06938 ( 2451) SS BOND : bond 0.00580 ( 34) SS BOND : angle 1.50492 ( 68) covalent geometry : bond 0.00313 (23102) covalent geometry : angle 0.63390 (31428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5735 (OUTLIER) cc_final: 0.5312 (t-90) REVERT: A 195 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6500 (tt) REVERT: A 960 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (mp) REVERT: A 981 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7074 (t) REVERT: B 189 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7226 (tmm-80) REVERT: B 418 THR cc_start: 0.8516 (m) cc_final: 0.7936 (t) REVERT: B 948 GLN cc_start: 0.8481 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 221 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: C 263 PHE cc_start: 0.8013 (m-10) cc_final: 0.7793 (m-10) REVERT: C 747 ASN cc_start: 0.7812 (m-40) cc_final: 0.7422 (t0) outliers start: 66 outliers final: 32 residues processed: 219 average time/residue: 0.2891 time to fit residues: 105.6015 Evaluate side-chains 189 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 897 ASN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 956 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 46 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.108052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082414 restraints weight = 70580.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081595 restraints weight = 61433.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082395 restraints weight = 48989.422| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23190 Z= 0.187 Angle : 0.677 14.061 31658 Z= 0.338 Chirality : 0.048 0.524 3724 Planarity : 0.005 0.061 4024 Dihedral : 7.315 59.544 4129 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 4.08 % Allowed : 19.84 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.15), residues: 2784 helix: 1.96 (0.21), residues: 591 sheet: -0.10 (0.21), residues: 514 loop : -1.32 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 246 HIS 0.003 0.001 HIS B1047 PHE 0.030 0.002 PHE B 579 TYR 0.018 0.002 TYR C1050 ARG 0.015 0.001 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 35) link_NAG-ASN : angle 3.38891 ( 105) link_BETA1-4 : bond 0.00425 ( 19) link_BETA1-4 : angle 1.75588 ( 57) hydrogen bonds : bond 0.05169 ( 868) hydrogen bonds : angle 5.99063 ( 2451) SS BOND : bond 0.00394 ( 34) SS BOND : angle 1.62279 ( 68) covalent geometry : bond 0.00429 (23102) covalent geometry : angle 0.64209 (31428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 153 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.5065 (t-90) REVERT: A 195 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6333 (tt) REVERT: A 307 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5745 (mtp-110) REVERT: A 680 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7878 (mtm) REVERT: A 960 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 981 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7209 (t) REVERT: B 189 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7275 (tmm-80) REVERT: B 232 PHE cc_start: 0.5821 (t80) cc_final: 0.5609 (t80) REVERT: B 598 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8156 (tt) REVERT: B 948 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8203 (tp-100) REVERT: C 102 TRP cc_start: 0.6277 (m-90) cc_final: 0.6049 (m-90) REVERT: C 236 LEU cc_start: 0.7447 (mm) cc_final: 0.7102 (mt) REVERT: C 263 PHE cc_start: 0.8031 (m-10) cc_final: 0.7789 (m-10) REVERT: C 519 ASP cc_start: 0.6314 (OUTLIER) cc_final: 0.5669 (t0) REVERT: C 747 ASN cc_start: 0.7912 (m-40) cc_final: 0.7469 (t0) REVERT: C 837 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6799 (mttt) REVERT: C 979 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8567 (mt) outliers start: 100 outliers final: 62 residues processed: 234 average time/residue: 0.2962 time to fit residues: 117.5187 Evaluate side-chains 212 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 139 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 477 TRP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 838 PHE Chi-restraints excluded: chain B residue 839 ASN Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 897 ASN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 204 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN C 33 GLN C 897 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082242 restraints weight = 71187.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080965 restraints weight = 58609.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081509 restraints weight = 51025.379| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23190 Z= 0.160 Angle : 0.652 12.961 31658 Z= 0.322 Chirality : 0.047 0.496 3724 Planarity : 0.005 0.061 4024 Dihedral : 6.891 57.810 4128 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 4.04 % Allowed : 20.37 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.15), residues: 2784 helix: 1.99 (0.21), residues: 590 sheet: -0.19 (0.21), residues: 531 loop : -1.31 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 246 HIS 0.005 0.001 HIS B 446 PHE 0.024 0.002 PHE B 579 TYR 0.029 0.002 TYR A 253 ARG 0.007 0.000 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 35) link_NAG-ASN : angle 3.24324 ( 105) link_BETA1-4 : bond 0.00424 ( 19) link_BETA1-4 : angle 1.67775 ( 57) hydrogen bonds : bond 0.04773 ( 868) hydrogen bonds : angle 5.84333 ( 2451) SS BOND : bond 0.00386 ( 34) SS BOND : angle 1.49417 ( 68) covalent geometry : bond 0.00367 (23102) covalent geometry : angle 0.61859 (31428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 158 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5712 (OUTLIER) cc_final: 0.5144 (t-90) REVERT: A 195 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6365 (tt) REVERT: A 680 MET cc_start: 0.8037 (mtm) cc_final: 0.7828 (mtm) REVERT: A 714 MET cc_start: 0.8009 (ttt) cc_final: 0.7680 (ttp) REVERT: A 960 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 189 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7372 (tmm-80) REVERT: B 232 PHE cc_start: 0.6132 (t80) cc_final: 0.5878 (t80) REVERT: B 598 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8156 (tt) REVERT: B 948 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8075 (tp-100) REVERT: C 199 SER cc_start: 0.8532 (m) cc_final: 0.8064 (t) REVERT: C 236 LEU cc_start: 0.7475 (mm) cc_final: 0.7197 (mt) REVERT: C 519 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.5916 (t0) REVERT: C 716 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7313 (mtpp) REVERT: C 747 ASN cc_start: 0.7861 (m-40) cc_final: 0.7455 (t0) REVERT: C 762 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: C 979 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8580 (mt) outliers start: 99 outliers final: 65 residues processed: 242 average time/residue: 0.2921 time to fit residues: 118.0464 Evaluate side-chains 216 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 838 PHE Chi-restraints excluded: chain B residue 839 ASN Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 762 ARG Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 170 optimal weight: 1.9990 chunk 165 optimal weight: 0.0010 chunk 178 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 600 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.108430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083224 restraints weight = 70840.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082404 restraints weight = 61507.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082936 restraints weight = 52866.641| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23190 Z= 0.134 Angle : 0.620 12.077 31658 Z= 0.307 Chirality : 0.046 0.463 3724 Planarity : 0.004 0.061 4024 Dihedral : 6.375 57.974 4126 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 4.41 % Allowed : 20.04 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.15), residues: 2784 helix: 2.15 (0.21), residues: 590 sheet: -0.18 (0.21), residues: 531 loop : -1.26 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 246 HIS 0.005 0.001 HIS C1066 PHE 0.022 0.001 PHE C 73 TYR 0.021 0.001 TYR A 253 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 35) link_NAG-ASN : angle 3.11884 ( 105) link_BETA1-4 : bond 0.00415 ( 19) link_BETA1-4 : angle 1.62561 ( 57) hydrogen bonds : bond 0.04439 ( 868) hydrogen bonds : angle 5.66104 ( 2451) SS BOND : bond 0.00317 ( 34) SS BOND : angle 1.32856 ( 68) covalent geometry : bond 0.00304 (23102) covalent geometry : angle 0.58788 (31428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 160 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.5195 (t-90) REVERT: A 195 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6210 (tt) REVERT: A 317 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6516 (t80) REVERT: A 680 MET cc_start: 0.8049 (mtm) cc_final: 0.7826 (mtm) REVERT: A 714 MET cc_start: 0.8043 (ttt) cc_final: 0.7713 (ttp) REVERT: A 960 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 973 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 1122 ASP cc_start: 0.8223 (t0) cc_final: 0.7897 (t0) REVERT: B 189 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7242 (tmm-80) REVERT: B 598 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8111 (tt) REVERT: B 948 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8086 (tp-100) REVERT: C 199 SER cc_start: 0.8621 (m) cc_final: 0.8179 (t) REVERT: C 519 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.5961 (t0) REVERT: C 747 ASN cc_start: 0.7827 (m-40) cc_final: 0.7350 (t0) REVERT: C 837 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6722 (mptt) REVERT: C 979 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8443 (mt) outliers start: 108 outliers final: 67 residues processed: 251 average time/residue: 0.2913 time to fit residues: 123.6907 Evaluate side-chains 220 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 144 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 838 PHE Chi-restraints excluded: chain B residue 839 ASN Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 987 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 122 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.107402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082123 restraints weight = 70702.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081597 restraints weight = 58169.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082113 restraints weight = 44817.151| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23190 Z= 0.174 Angle : 0.655 11.936 31658 Z= 0.324 Chirality : 0.047 0.461 3724 Planarity : 0.005 0.060 4024 Dihedral : 6.492 58.469 4126 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 5.02 % Allowed : 20.04 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.15), residues: 2784 helix: 1.98 (0.21), residues: 596 sheet: -0.15 (0.22), residues: 532 loop : -1.38 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 246 HIS 0.006 0.001 HIS B 446 PHE 0.024 0.002 PHE C 162 TYR 0.017 0.001 TYR A 253 ARG 0.008 0.000 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 35) link_NAG-ASN : angle 3.12492 ( 105) link_BETA1-4 : bond 0.00438 ( 19) link_BETA1-4 : angle 1.67887 ( 57) hydrogen bonds : bond 0.04669 ( 868) hydrogen bonds : angle 5.77727 ( 2451) SS BOND : bond 0.00357 ( 34) SS BOND : angle 1.37746 ( 68) covalent geometry : bond 0.00400 (23102) covalent geometry : angle 0.62465 (31428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 156 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5519 (OUTLIER) cc_final: 0.4942 (t-90) REVERT: A 195 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6121 (tt) REVERT: A 295 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5552 (pm20) REVERT: A 317 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6568 (t80) REVERT: A 714 MET cc_start: 0.8051 (ttt) cc_final: 0.7728 (ttp) REVERT: A 947 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (mptt) REVERT: A 960 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 189 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7243 (tmm-80) REVERT: B 598 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8114 (tt) REVERT: B 948 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8116 (tp-100) REVERT: C 199 SER cc_start: 0.8614 (m) cc_final: 0.8196 (t) REVERT: C 236 LEU cc_start: 0.7349 (mm) cc_final: 0.7034 (mt) REVERT: C 519 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6207 (t0) REVERT: C 716 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7227 (mtpp) REVERT: C 747 ASN cc_start: 0.7832 (m-40) cc_final: 0.7363 (t0) REVERT: C 798 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6623 (mtm180) REVERT: C 837 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6671 (mptt) REVERT: C 979 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8551 (mt) outliers start: 123 outliers final: 94 residues processed: 257 average time/residue: 0.3076 time to fit residues: 131.6756 Evaluate side-chains 250 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 143 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 838 PHE Chi-restraints excluded: chain B residue 839 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 798 ARG Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 213 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 135 optimal weight: 0.0060 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 264 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 102 optimal weight: 0.1980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.108519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083184 restraints weight = 71226.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082845 restraints weight = 58489.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083564 restraints weight = 44909.464| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23190 Z= 0.124 Angle : 0.607 10.950 31658 Z= 0.299 Chirality : 0.045 0.424 3724 Planarity : 0.004 0.060 4024 Dihedral : 6.080 58.902 4126 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 4.20 % Allowed : 21.02 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.15), residues: 2784 helix: 2.36 (0.21), residues: 584 sheet: -0.19 (0.22), residues: 542 loop : -1.30 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 246 HIS 0.009 0.001 HIS C1066 PHE 0.021 0.001 PHE C 73 TYR 0.017 0.001 TYR A 253 ARG 0.008 0.000 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 35) link_NAG-ASN : angle 2.97348 ( 105) link_BETA1-4 : bond 0.00428 ( 19) link_BETA1-4 : angle 1.57176 ( 57) hydrogen bonds : bond 0.04141 ( 868) hydrogen bonds : angle 5.51333 ( 2451) SS BOND : bond 0.00284 ( 34) SS BOND : angle 1.20390 ( 68) covalent geometry : bond 0.00285 (23102) covalent geometry : angle 0.57758 (31428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 163 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5504 (OUTLIER) cc_final: 0.4918 (t-90) REVERT: A 295 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5665 (pm20) REVERT: A 317 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6516 (t80) REVERT: A 714 MET cc_start: 0.8017 (ttt) cc_final: 0.7720 (ttp) REVERT: A 960 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 189 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7262 (tmm-80) REVERT: B 598 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7952 (tt) REVERT: B 948 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8045 (tp-100) REVERT: C 199 SER cc_start: 0.8665 (m) cc_final: 0.8273 (t) REVERT: C 519 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6273 (t0) REVERT: C 716 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7387 (mtmt) REVERT: C 747 ASN cc_start: 0.7669 (m-40) cc_final: 0.7223 (t0) REVERT: C 837 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6645 (mptt) REVERT: C 979 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8507 (mt) outliers start: 103 outliers final: 73 residues processed: 247 average time/residue: 0.3001 time to fit residues: 124.2306 Evaluate side-chains 241 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 158 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 852 MET Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1116 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 108 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 196 optimal weight: 0.3980 chunk 173 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.107403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081339 restraints weight = 70878.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081189 restraints weight = 52570.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081260 restraints weight = 40977.656| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23190 Z= 0.151 Angle : 0.632 11.114 31658 Z= 0.311 Chirality : 0.046 0.430 3724 Planarity : 0.004 0.060 4024 Dihedral : 6.117 59.248 4126 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 4.53 % Allowed : 20.53 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.15), residues: 2784 helix: 2.20 (0.21), residues: 595 sheet: -0.21 (0.22), residues: 537 loop : -1.35 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 246 HIS 0.007 0.001 HIS C1066 PHE 0.019 0.001 PHE B 579 TYR 0.016 0.001 TYR A 887 ARG 0.008 0.000 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 35) link_NAG-ASN : angle 2.99434 ( 105) link_BETA1-4 : bond 0.00426 ( 19) link_BETA1-4 : angle 1.66148 ( 57) hydrogen bonds : bond 0.04378 ( 868) hydrogen bonds : angle 5.59005 ( 2451) SS BOND : bond 0.00356 ( 34) SS BOND : angle 1.28168 ( 68) covalent geometry : bond 0.00348 (23102) covalent geometry : angle 0.60281 (31428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 163 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5610 (OUTLIER) cc_final: 0.4992 (t-90) REVERT: A 195 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6097 (tt) REVERT: A 295 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5660 (pm20) REVERT: A 317 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6585 (t80) REVERT: A 714 MET cc_start: 0.8062 (ttt) cc_final: 0.7726 (ttp) REVERT: A 960 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 189 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7534 (tmm-80) REVERT: B 307 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7320 (ttp-110) REVERT: B 598 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7978 (tt) REVERT: B 745 GLN cc_start: 0.8036 (mp10) cc_final: 0.7539 (mp10) REVERT: B 948 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8112 (tp-100) REVERT: C 199 SER cc_start: 0.8674 (m) cc_final: 0.8310 (t) REVERT: C 264 MET cc_start: 0.5978 (tmm) cc_final: 0.5764 (tmm) REVERT: C 519 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6312 (t0) REVERT: C 716 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7343 (mtmt) REVERT: C 747 ASN cc_start: 0.7720 (m-40) cc_final: 0.7326 (t0) REVERT: C 798 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6508 (mtm180) REVERT: C 837 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6591 (mptt) REVERT: C 979 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8517 (mt) outliers start: 111 outliers final: 85 residues processed: 255 average time/residue: 0.2999 time to fit residues: 127.6872 Evaluate side-chains 245 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 148 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 838 PHE Chi-restraints excluded: chain B residue 839 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 798 ARG Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 852 MET Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 267 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 136 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.108538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.083952 restraints weight = 70447.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083186 restraints weight = 64922.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083736 restraints weight = 52255.151| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.003 0.059 23190 Z= 0.119 Angle : 0.616 10.520 31658 Z= 0.301 Chirality : 0.046 0.409 3724 Planarity : 0.004 0.060 4024 Dihedral : 5.851 59.610 4126 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 3.92 % Allowed : 21.10 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.15), residues: 2784 helix: 2.34 (0.21), residues: 596 sheet: -0.18 (0.22), residues: 536 loop : -1.32 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 246 HIS 0.007 0.001 HIS C1066 PHE 0.027 0.001 PHE C 73 TYR 0.015 0.001 TYR A 253 ARG 0.009 0.000 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 35) link_NAG-ASN : angle 2.91415 ( 105) link_BETA1-4 : bond 0.00433 ( 19) link_BETA1-4 : angle 1.59982 ( 57) hydrogen bonds : bond 0.04086 ( 868) hydrogen bonds : angle 5.43573 ( 2451) SS BOND : bond 0.00319 ( 34) SS BOND : angle 1.18659 ( 68) covalent geometry : bond 0.00274 (23102) covalent geometry : angle 0.58851 (31428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 168 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5591 (OUTLIER) cc_final: 0.5152 (t-90) REVERT: A 195 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.5942 (tt) REVERT: A 295 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5770 (pm20) REVERT: A 317 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6557 (t80) REVERT: A 714 MET cc_start: 0.8029 (ttt) cc_final: 0.7731 (ttp) REVERT: A 960 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 967 LEU cc_start: 0.7325 (tt) cc_final: 0.6847 (mm) REVERT: B 189 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7200 (tmm-80) REVERT: B 598 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 745 GLN cc_start: 0.8049 (mp10) cc_final: 0.7521 (mp10) REVERT: B 948 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 199 SER cc_start: 0.8709 (m) cc_final: 0.8358 (t) REVERT: C 236 LEU cc_start: 0.7290 (mm) cc_final: 0.6968 (mt) REVERT: C 294 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7877 (t80) REVERT: C 519 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6269 (t0) REVERT: C 747 ASN cc_start: 0.7845 (m-40) cc_final: 0.7303 (t0) REVERT: C 798 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6518 (mtm180) REVERT: C 837 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6557 (mptt) REVERT: C 979 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8476 (mt) outliers start: 96 outliers final: 75 residues processed: 250 average time/residue: 0.3079 time to fit residues: 129.3158 Evaluate side-chains 240 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 153 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 798 ARG Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1116 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 19 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 228 optimal weight: 0.1980 chunk 177 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.108873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084210 restraints weight = 70569.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083176 restraints weight = 63451.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083752 restraints weight = 50144.296| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23190 Z= 0.115 Angle : 0.611 11.050 31658 Z= 0.298 Chirality : 0.045 0.400 3724 Planarity : 0.004 0.060 4024 Dihedral : 5.619 59.576 4126 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 3.63 % Allowed : 21.55 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.16), residues: 2784 helix: 2.42 (0.21), residues: 596 sheet: -0.16 (0.22), residues: 548 loop : -1.30 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 246 HIS 0.007 0.001 HIS C1066 PHE 0.019 0.001 PHE B 579 TYR 0.015 0.001 TYR A 253 ARG 0.010 0.000 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 35) link_NAG-ASN : angle 2.89211 ( 105) link_BETA1-4 : bond 0.00423 ( 19) link_BETA1-4 : angle 1.60356 ( 57) hydrogen bonds : bond 0.03957 ( 868) hydrogen bonds : angle 5.35472 ( 2451) SS BOND : bond 0.00295 ( 34) SS BOND : angle 1.16340 ( 68) covalent geometry : bond 0.00266 (23102) covalent geometry : angle 0.58376 (31428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 164 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5709 (OUTLIER) cc_final: 0.5229 (t-90) REVERT: A 295 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5862 (pm20) REVERT: A 317 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6600 (t80) REVERT: A 714 MET cc_start: 0.8008 (ttt) cc_final: 0.7707 (ttp) REVERT: A 947 LYS cc_start: 0.8222 (mptt) cc_final: 0.8019 (mptt) REVERT: A 967 LEU cc_start: 0.7429 (tt) cc_final: 0.6873 (mm) REVERT: B 189 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7206 (tmm-80) REVERT: B 477 TRP cc_start: 0.5031 (m100) cc_final: 0.4758 (t-100) REVERT: B 598 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8240 (tp) REVERT: B 745 GLN cc_start: 0.8042 (mp10) cc_final: 0.7494 (mp10) REVERT: B 948 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 199 SER cc_start: 0.8696 (m) cc_final: 0.8361 (t) REVERT: C 236 LEU cc_start: 0.7256 (mm) cc_final: 0.7017 (mt) REVERT: C 294 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.7878 (t80) REVERT: C 519 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6311 (t0) REVERT: C 747 ASN cc_start: 0.7656 (m-40) cc_final: 0.7229 (t0) REVERT: C 798 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6492 (mtm180) REVERT: C 837 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6503 (mptt) REVERT: C 979 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8447 (mt) outliers start: 89 outliers final: 72 residues processed: 239 average time/residue: 0.3116 time to fit residues: 123.7567 Evaluate side-chains 239 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 838 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 798 ARG Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1116 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 94 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.106321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081309 restraints weight = 71139.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080569 restraints weight = 63228.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081332 restraints weight = 49180.074| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 23190 Z= 0.218 Angle : 0.701 12.188 31658 Z= 0.346 Chirality : 0.048 0.436 3724 Planarity : 0.005 0.060 4024 Dihedral : 6.316 59.994 4124 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.43 % Rotamer: Outliers : 4.04 % Allowed : 21.31 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.15), residues: 2784 helix: 1.88 (0.21), residues: 603 sheet: -0.24 (0.22), residues: 537 loop : -1.43 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 246 HIS 0.007 0.001 HIS C1066 PHE 0.042 0.002 PHE C 73 TYR 0.019 0.002 TYR C 267 ARG 0.010 0.001 ARG C 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 35) link_NAG-ASN : angle 3.01369 ( 105) link_BETA1-4 : bond 0.00442 ( 19) link_BETA1-4 : angle 1.79049 ( 57) hydrogen bonds : bond 0.04821 ( 868) hydrogen bonds : angle 5.78648 ( 2451) SS BOND : bond 0.00401 ( 34) SS BOND : angle 1.48136 ( 68) covalent geometry : bond 0.00510 (23102) covalent geometry : angle 0.67348 (31428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.63 seconds wall clock time: 109 minutes 7.69 seconds (6547.69 seconds total)