Starting phenix.real_space_refine on Sun Oct 12 08:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wly_37635/10_2025/8wly_37635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wly_37635/10_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_37635/10_2025/8wly_37635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wly_37635/10_2025/8wly_37635.map" model { file = "/net/cci-nas-00/data/ceres_data/8wly_37635/10_2025/8wly_37635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wly_37635/10_2025/8wly_37635_neut.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.71, per 1000 atoms: 0.25 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: 1.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.11 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: 5.66 Time building geometry restraints manager: 2.19 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 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.150 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (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 ARG 0.005 0.001 ARG B 345 TYR 0.024 0.002 TYR A 887 PHE 0.023 0.002 PHE B 77 TRP 0.034 0.002 TRP C 246 HIS 0.007 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00468 (23102) covalent geometry : angle 0.85305 (31428) SS BOND : bond 0.00703 ( 34) SS BOND : angle 1.38698 ( 68) hydrogen bonds : bond 0.15967 ( 868) hydrogen bonds : angle 7.43268 ( 2451) link_BETA1-4 : bond 0.00663 ( 19) link_BETA1-4 : angle 1.92726 ( 57) link_NAG-ASN : bond 0.00768 ( 35) link_NAG-ASN : angle 3.95107 ( 105) *********************** 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 : 0.875 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: 0.8036 (mtm180) REVERT: C 106 SER cc_start: 0.4163 (OUTLIER) cc_final: 0.3649 (t) REVERT: C 108 MET cc_start: 0.3777 (OUTLIER) cc_final: 0.2080 (ttm) 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: 0.1530 time to fit residues: 54.3316 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 : 0.850 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 745 GLN C 747 ASN C 897 ASN C 988 GLN C1006 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.108201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.082663 restraints weight = 70906.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081704 restraints weight = 55552.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082251 restraints weight = 45001.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082448 restraints weight = 38685.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082589 restraints weight = 36346.406| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23190 Z= 0.190 Angle : 0.713 14.940 31658 Z= 0.357 Chirality : 0.049 0.559 3724 Planarity : 0.005 0.062 4024 Dihedral : 8.369 59.789 4135 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 3.39 % Allowed : 20.41 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 2784 helix: 1.85 (0.21), residues: 598 sheet: -0.14 (0.21), residues: 520 loop : -1.37 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1002 TYR 0.022 0.002 TYR B 409 PHE 0.026 0.002 PHE B 579 TRP 0.017 0.002 TRP C 246 HIS 0.005 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00433 (23102) covalent geometry : angle 0.67755 (31428) SS BOND : bond 0.00499 ( 34) SS BOND : angle 1.61835 ( 68) hydrogen bonds : bond 0.05612 ( 868) hydrogen bonds : angle 6.23981 ( 2451) link_BETA1-4 : bond 0.00421 ( 19) link_BETA1-4 : angle 1.77644 ( 57) link_NAG-ASN : bond 0.00707 ( 35) link_NAG-ASN : angle 3.53112 ( 105) *********************** 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 235 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 152 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5856 (OUTLIER) cc_final: 0.5396 (t-90) REVERT: A 195 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6425 (tt) REVERT: A 960 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 981 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7020 (t) REVERT: B 153 ILE cc_start: 0.6824 (mm) cc_final: 0.6576 (pt) REVERT: B 189 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7164 (tmm-80) REVERT: B 418 THR cc_start: 0.8592 (m) cc_final: 0.8018 (t) REVERT: B 948 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8262 (tp-100) REVERT: C 263 PHE cc_start: 0.8073 (m-10) cc_final: 0.7832 (m-10) REVERT: C 747 ASN cc_start: 0.7850 (m-40) cc_final: 0.7462 (t0) REVERT: C 979 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8608 (mt) outliers start: 83 outliers final: 47 residues processed: 219 average time/residue: 0.1307 time to fit residues: 48.3279 Evaluate side-chains 196 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 192 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 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 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 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 598 LEU Chi-restraints excluded: chain B residue 730 THR 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 1026 CYS Chi-restraints excluded: chain B residue 1105 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 304 SER 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 721 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 786 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 188 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 940 GLN C 54 HIS C 136 ASN C 897 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.106876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081758 restraints weight = 72052.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080610 restraints weight = 67359.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081119 restraints weight = 53884.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081384 restraints weight = 46387.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081533 restraints weight = 42277.509| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23190 Z= 0.224 Angle : 0.719 14.405 31658 Z= 0.360 Chirality : 0.049 0.538 3724 Planarity : 0.005 0.061 4024 Dihedral : 7.649 59.609 4127 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 4.78 % Allowed : 19.51 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 2784 helix: 1.69 (0.21), residues: 593 sheet: -0.31 (0.22), residues: 522 loop : -1.41 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 966 TYR 0.019 0.002 TYR C1050 PHE 0.019 0.002 PHE C 239 TRP 0.018 0.002 TRP C 246 HIS 0.004 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00512 (23102) covalent geometry : angle 0.68330 (31428) SS BOND : bond 0.00405 ( 34) SS BOND : angle 1.72842 ( 68) hydrogen bonds : bond 0.05520 ( 868) hydrogen bonds : angle 6.20495 ( 2451) link_BETA1-4 : bond 0.00452 ( 19) link_BETA1-4 : angle 1.78769 ( 57) link_NAG-ASN : bond 0.00731 ( 35) link_NAG-ASN : angle 3.49827 ( 105) *********************** 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 273 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 156 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.5088 (t-90) REVERT: A 195 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6254 (tt) REVERT: A 307 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.6046 (tpt90) REVERT: A 960 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 981 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7163 (t) REVERT: B 153 ILE cc_start: 0.6962 (mm) cc_final: 0.6560 (pt) REVERT: B 189 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7141 (tmm-80) REVERT: B 357 TYR cc_start: 0.6703 (t80) cc_final: 0.6476 (t80) REVERT: B 598 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8219 (tt) REVERT: B 948 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8145 (tp-100) REVERT: C 102 TRP cc_start: 0.6322 (m-90) cc_final: 0.6115 (m-90) REVERT: C 263 PHE cc_start: 0.8030 (m-10) cc_final: 0.7736 (m-10) REVERT: C 519 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.5761 (t0) REVERT: C 716 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7405 (mtpp) REVERT: C 747 ASN cc_start: 0.7831 (m-40) cc_final: 0.7447 (t0) REVERT: C 798 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6732 (mtm180) REVERT: C 837 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6785 (mttt) REVERT: C 979 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8665 (mt) outliers start: 117 outliers final: 69 residues processed: 251 average time/residue: 0.1307 time to fit residues: 55.1998 Evaluate side-chains 224 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 143 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 118 MET 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 300 ILE Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 605 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 851 ASP 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 A residue 1064 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 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 413 LEU Chi-restraints excluded: chain B residue 477 TRP Chi-restraints excluded: chain B residue 518 THR 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 723 MET 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 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1103 THR 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 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 716 LYS Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 755 VAL 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 1119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 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 = 0.108390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083352 restraints weight = 70686.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082694 restraints weight = 61991.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083148 restraints weight = 52084.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083435 restraints weight = 41246.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083540 restraints weight = 38078.040| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1849 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= 0.128 Angle : 0.623 12.529 31658 Z= 0.310 Chirality : 0.046 0.476 3724 Planarity : 0.004 0.062 4024 Dihedral : 6.703 59.232 4126 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 3.84 % Allowed : 20.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 2784 helix: 2.08 (0.21), residues: 594 sheet: -0.22 (0.21), residues: 528 loop : -1.33 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 966 TYR 0.030 0.001 TYR A 253 PHE 0.019 0.001 PHE C 73 TRP 0.017 0.002 TRP C 246 HIS 0.006 0.001 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00287 (23102) covalent geometry : angle 0.59020 (31428) SS BOND : bond 0.00441 ( 34) SS BOND : angle 1.39406 ( 68) hydrogen bonds : bond 0.04511 ( 868) hydrogen bonds : angle 5.74144 ( 2451) link_BETA1-4 : bond 0.00426 ( 19) link_BETA1-4 : angle 1.63438 ( 57) link_NAG-ASN : bond 0.00653 ( 35) link_NAG-ASN : angle 3.19997 ( 105) *********************** 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 269 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 175 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.5303 (t-90) REVERT: A 195 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6237 (tt) REVERT: A 317 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6546 (t80) REVERT: A 714 MET cc_start: 0.8063 (ttt) cc_final: 0.7768 (ttp) REVERT: A 960 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 153 ILE cc_start: 0.6741 (mm) cc_final: 0.6409 (pt) REVERT: B 189 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7206 (tmm-80) REVERT: B 353 TYR cc_start: 0.5256 (OUTLIER) cc_final: 0.4712 (t80) REVERT: B 948 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8177 (tp-100) REVERT: C 199 SER cc_start: 0.8548 (m) cc_final: 0.8099 (t) REVERT: C 236 LEU cc_start: 0.7274 (mm) cc_final: 0.6961 (mt) REVERT: C 263 PHE cc_start: 0.7971 (m-10) cc_final: 0.7692 (m-10) REVERT: C 519 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.5882 (t0) REVERT: C 747 ASN cc_start: 0.7752 (m-40) cc_final: 0.7282 (t0) REVERT: C 837 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6806 (mttt) REVERT: C 979 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8576 (mt) outliers start: 94 outliers final: 52 residues processed: 256 average time/residue: 0.1360 time to fit residues: 57.8547 Evaluate side-chains 213 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 124 LEU 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 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 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 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 124 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 300 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 590 ASN 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 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 956 ILE 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 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 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 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1097 ILE 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 258 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 135 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 146 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 745 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.108785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083612 restraints weight = 70386.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082880 restraints weight = 59477.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083431 restraints weight = 46580.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083877 restraints weight = 39883.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083814 restraints weight = 37946.980| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2065 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= 0.117 Angle : 0.610 11.878 31658 Z= 0.301 Chirality : 0.045 0.457 3724 Planarity : 0.004 0.062 4024 Dihedral : 6.209 58.711 4126 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 4.00 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 2784 helix: 2.38 (0.21), residues: 582 sheet: -0.14 (0.21), residues: 539 loop : -1.29 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 966 TYR 0.020 0.001 TYR A 253 PHE 0.014 0.001 PHE B 579 TRP 0.023 0.002 TRP C 246 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00267 (23102) covalent geometry : angle 0.57848 (31428) SS BOND : bond 0.00278 ( 34) SS BOND : angle 1.23494 ( 68) hydrogen bonds : bond 0.04238 ( 868) hydrogen bonds : angle 5.56287 ( 2451) link_BETA1-4 : bond 0.00416 ( 19) link_BETA1-4 : angle 1.61663 ( 57) link_NAG-ASN : bond 0.00635 ( 35) link_NAG-ASN : angle 3.10081 ( 105) *********************** 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 261 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 163 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5734 (OUTLIER) cc_final: 0.5299 (t-90) REVERT: A 195 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6233 (tt) REVERT: A 295 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5523 (pm20) REVERT: A 317 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6451 (t80) REVERT: A 714 MET cc_start: 0.8026 (ttt) cc_final: 0.7704 (ttp) REVERT: A 947 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7794 (mptt) REVERT: A 960 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 1122 ASP cc_start: 0.8289 (t0) cc_final: 0.7971 (t0) REVERT: B 153 ILE cc_start: 0.6725 (mm) cc_final: 0.6401 (pt) REVERT: B 189 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7244 (tmm-80) REVERT: B 353 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.4777 (t80) REVERT: B 948 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 199 SER cc_start: 0.8622 (m) cc_final: 0.8182 (t) REVERT: C 236 LEU cc_start: 0.7298 (mm) cc_final: 0.7007 (mt) REVERT: C 519 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.5949 (t0) REVERT: C 747 ASN cc_start: 0.7748 (m-40) cc_final: 0.7389 (t0) REVERT: C 837 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6746 (mptt) REVERT: C 979 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8429 (mt) outliers start: 98 outliers final: 62 residues processed: 247 average time/residue: 0.1246 time to fit residues: 52.0810 Evaluate side-chains 229 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 156 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 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 713 SER Chi-restraints excluded: chain A residue 774 THR 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 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 287 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 THR 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 590 ASN 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 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 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 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 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 202 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 264 optimal weight: 4.9990 chunk 271 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.106182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080339 restraints weight = 71180.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079552 restraints weight = 55324.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079766 restraints weight = 44716.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080025 restraints weight = 41627.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080206 restraints weight = 37205.559| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23190 Z= 0.214 Angle : 0.701 12.291 31658 Z= 0.347 Chirality : 0.048 0.475 3724 Planarity : 0.005 0.060 4024 Dihedral : 6.732 59.535 4126 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 5.22 % Allowed : 20.08 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 2784 helix: 1.84 (0.21), residues: 596 sheet: -0.25 (0.21), residues: 537 loop : -1.43 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 307 TYR 0.020 0.002 TYR C1050 PHE 0.026 0.002 PHE C 162 TRP 0.021 0.002 TRP C 246 HIS 0.008 0.001 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00493 (23102) covalent geometry : angle 0.67010 (31428) SS BOND : bond 0.00521 ( 34) SS BOND : angle 1.47243 ( 68) hydrogen bonds : bond 0.05036 ( 868) hydrogen bonds : angle 5.93227 ( 2451) link_BETA1-4 : bond 0.00432 ( 19) link_BETA1-4 : angle 1.80475 ( 57) link_NAG-ASN : bond 0.00697 ( 35) link_NAG-ASN : angle 3.22202 ( 105) *********************** 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 277 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 149 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5570 (OUTLIER) cc_final: 0.4981 (t-90) REVERT: A 195 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6249 (tt) REVERT: A 295 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5614 (pm20) REVERT: A 317 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6609 (t80) REVERT: A 714 MET cc_start: 0.8004 (ttt) cc_final: 0.7667 (ttp) REVERT: A 960 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 189 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7488 (tmm-80) REVERT: B 598 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 948 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8317 (tp-100) REVERT: C 199 SER cc_start: 0.8521 (m) cc_final: 0.8091 (t) REVERT: C 519 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6301 (t0) REVERT: C 716 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7332 (mtpp) REVERT: C 747 ASN cc_start: 0.7706 (m-40) cc_final: 0.7353 (t0) REVERT: C 837 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6743 (mptt) REVERT: C 979 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8578 (mt) outliers start: 128 outliers final: 93 residues processed: 260 average time/residue: 0.1223 time to fit residues: 53.6238 Evaluate side-chains 246 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 142 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain A residue 124 LEU 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 284 LEU 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 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 605 THR 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 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 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 406 ILE Chi-restraints excluded: chain B residue 459 VAL 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 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 730 THR Chi-restraints excluded: chain B residue 774 THR 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 860 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 956 ILE Chi-restraints excluded: chain B residue 967 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 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 304 SER 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 680 MET 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 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 841 LEU 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 1023 VAL 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 186 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 226 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN ** B1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.105883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080446 restraints weight = 71327.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079604 restraints weight = 64051.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080145 restraints weight = 50644.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080369 restraints weight = 43625.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080528 restraints weight = 38350.759| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23190 Z= 0.216 Angle : 0.702 11.661 31658 Z= 0.348 Chirality : 0.048 0.449 3724 Planarity : 0.005 0.060 4024 Dihedral : 6.953 59.811 4126 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 5.06 % Allowed : 20.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 2784 helix: 1.65 (0.21), residues: 602 sheet: -0.36 (0.21), residues: 544 loop : -1.58 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 966 TYR 0.017 0.002 TYR C1050 PHE 0.022 0.002 PHE C 162 TRP 0.031 0.002 TRP C 246 HIS 0.012 0.001 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00496 (23102) covalent geometry : angle 0.67247 (31428) SS BOND : bond 0.00543 ( 34) SS BOND : angle 1.43684 ( 68) hydrogen bonds : bond 0.05033 ( 868) hydrogen bonds : angle 6.02136 ( 2451) link_BETA1-4 : bond 0.00442 ( 19) link_BETA1-4 : angle 1.77327 ( 57) link_NAG-ASN : bond 0.00683 ( 35) link_NAG-ASN : angle 3.16996 ( 105) *********************** 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 278 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 154 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5644 (OUTLIER) cc_final: 0.5054 (t-90) REVERT: A 195 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6012 (tt) REVERT: A 295 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5733 (pm20) REVERT: A 317 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6574 (t80) REVERT: A 714 MET cc_start: 0.8012 (ttt) cc_final: 0.7671 (ttp) REVERT: B 189 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7295 (tmm-80) REVERT: B 598 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 948 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8279 (tp-100) REVERT: C 199 SER cc_start: 0.8547 (m) cc_final: 0.8093 (t) REVERT: C 519 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6486 (t0) REVERT: C 710 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7471 (mtp) REVERT: C 716 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7474 (mtmt) REVERT: C 747 ASN cc_start: 0.7786 (m-40) cc_final: 0.7305 (t0) REVERT: C 798 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6797 (mtm180) REVERT: C 837 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6714 (mptt) REVERT: C 871 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7934 (p90) REVERT: C 979 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8616 (mt) outliers start: 124 outliers final: 91 residues processed: 261 average time/residue: 0.1250 time to fit residues: 54.7239 Evaluate side-chains 245 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 141 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 284 LEU 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 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 736 LEU 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 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 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 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 406 ILE Chi-restraints excluded: chain B residue 429 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 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 774 THR 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 956 ILE 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 262 THR 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 583 SER Chi-restraints excluded: chain C residue 629 VAL 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 710 MET Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 721 CYS 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 871 PHE 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 1023 VAL 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 226 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 767 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081228 restraints weight = 70750.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080812 restraints weight = 54505.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081350 restraints weight = 41326.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081691 restraints weight = 34918.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081745 restraints weight = 32056.244| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2795 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= 0.141 Angle : 0.639 10.850 31658 Z= 0.315 Chirality : 0.046 0.425 3724 Planarity : 0.005 0.060 4024 Dihedral : 6.490 57.570 4126 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 4.41 % Allowed : 20.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 2784 helix: 1.98 (0.21), residues: 596 sheet: -0.35 (0.21), residues: 539 loop : -1.50 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 966 TYR 0.017 0.001 TYR A 887 PHE 0.026 0.001 PHE C 73 TRP 0.049 0.002 TRP C 246 HIS 0.008 0.001 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00325 (23102) covalent geometry : angle 0.61054 (31428) SS BOND : bond 0.00514 ( 34) SS BOND : angle 1.27141 ( 68) hydrogen bonds : bond 0.04460 ( 868) hydrogen bonds : angle 5.75388 ( 2451) link_BETA1-4 : bond 0.00431 ( 19) link_BETA1-4 : angle 1.67769 ( 57) link_NAG-ASN : bond 0.00624 ( 35) link_NAG-ASN : angle 3.02204 ( 105) *********************** 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 266 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 158 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5706 (OUTLIER) cc_final: 0.5072 (t-90) REVERT: A 295 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5653 (pm20) REVERT: A 317 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 714 MET cc_start: 0.8023 (ttt) cc_final: 0.7744 (ttp) REVERT: B 189 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7383 (tmm-80) REVERT: B 264 MET cc_start: 0.6224 (tpp) cc_final: 0.5995 (tpp) REVERT: B 948 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7998 (tp-100) REVERT: C 199 SER cc_start: 0.8643 (m) cc_final: 0.8254 (t) REVERT: C 221 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6316 (t80) REVERT: C 519 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6333 (t0) REVERT: C 716 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7489 (mtmt) REVERT: C 723 MET cc_start: 0.8482 (mmm) cc_final: 0.8228 (mmm) REVERT: C 747 ASN cc_start: 0.7767 (m-40) cc_final: 0.7304 (t0) REVERT: C 837 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6587 (mptt) REVERT: C 871 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7896 (p90) REVERT: C 979 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8532 (mt) outliers start: 108 outliers final: 76 residues processed: 250 average time/residue: 0.1225 time to fit residues: 51.4125 Evaluate side-chains 229 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 143 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 232 PHE 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 518 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 570 GLU 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 960 LEU Chi-restraints excluded: chain A residue 971 GLU 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 221 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 353 TYR 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 459 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 638 ILE 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 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 956 ILE 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 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 223 LEU 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 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 871 PHE 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 1023 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082390 restraints weight = 70856.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081125 restraints weight = 67905.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081730 restraints weight = 55857.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081950 restraints weight = 46113.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082059 restraints weight = 42765.380| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23190 Z= 0.144 Angle : 0.637 10.751 31658 Z= 0.314 Chirality : 0.046 0.420 3724 Planarity : 0.005 0.060 4024 Dihedral : 6.313 57.195 4126 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 4.16 % Allowed : 21.27 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 2784 helix: 2.09 (0.21), residues: 595 sheet: -0.30 (0.22), residues: 535 loop : -1.50 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 966 TYR 0.014 0.001 TYR B 357 PHE 0.014 0.001 PHE B 579 TRP 0.040 0.002 TRP C 246 HIS 0.010 0.001 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00332 (23102) covalent geometry : angle 0.60800 (31428) SS BOND : bond 0.00369 ( 34) SS BOND : angle 1.34341 ( 68) hydrogen bonds : bond 0.04382 ( 868) hydrogen bonds : angle 5.68777 ( 2451) link_BETA1-4 : bond 0.00450 ( 19) link_BETA1-4 : angle 1.69714 ( 57) link_NAG-ASN : bond 0.00625 ( 35) link_NAG-ASN : angle 2.98906 ( 105) *********************** 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 256 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 154 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5638 (OUTLIER) cc_final: 0.5009 (t-90) REVERT: A 295 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5656 (pm20) REVERT: A 317 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 714 MET cc_start: 0.8002 (ttt) cc_final: 0.7719 (ttp) REVERT: A 967 LEU cc_start: 0.7434 (tt) cc_final: 0.7140 (mm) REVERT: A 971 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: B 598 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 948 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8220 (tp-100) REVERT: C 199 SER cc_start: 0.8704 (m) cc_final: 0.8320 (t) REVERT: C 519 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6396 (t0) REVERT: C 716 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7450 (mtmt) REVERT: C 723 MET cc_start: 0.8445 (mmm) cc_final: 0.8189 (mmm) REVERT: C 747 ASN cc_start: 0.7708 (m-40) cc_final: 0.7265 (t0) REVERT: C 837 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6523 (mptt) REVERT: C 871 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7889 (p90) REVERT: C 979 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8511 (mt) outliers start: 102 outliers final: 84 residues processed: 241 average time/residue: 0.1308 time to fit residues: 52.2768 Evaluate side-chains 239 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 145 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 124 LEU 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 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 540 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 851 ASP 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 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 272 THR 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 406 ILE Chi-restraints excluded: chain B residue 459 VAL 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 638 ILE 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 841 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 890 ASN Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1012 MET 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 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 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 644 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 786 SER Chi-restraints excluded: chain C residue 837 LYS Chi-restraints excluded: chain C residue 871 PHE 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 1023 VAL 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 141 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 0.0040 chunk 204 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 262 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.108081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082646 restraints weight = 70625.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082048 restraints weight = 56825.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082438 restraints weight = 43998.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082681 restraints weight = 40430.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082826 restraints weight = 35259.467| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23190 Z= 0.116 Angle : 0.615 10.412 31658 Z= 0.303 Chirality : 0.046 0.404 3724 Planarity : 0.004 0.060 4024 Dihedral : 5.867 57.374 4126 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 3.51 % Allowed : 21.92 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 2784 helix: 2.35 (0.21), residues: 595 sheet: -0.18 (0.21), residues: 540 loop : -1.44 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 966 TYR 0.020 0.001 TYR A 887 PHE 0.017 0.001 PHE B 162 TRP 0.041 0.002 TRP C 246 HIS 0.009 0.001 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00269 (23102) covalent geometry : angle 0.58773 (31428) SS BOND : bond 0.00279 ( 34) SS BOND : angle 1.18018 ( 68) hydrogen bonds : bond 0.04034 ( 868) hydrogen bonds : angle 5.48632 ( 2451) link_BETA1-4 : bond 0.00438 ( 19) link_BETA1-4 : angle 1.61380 ( 57) link_NAG-ASN : bond 0.00609 ( 35) link_NAG-ASN : angle 2.89316 ( 105) ********************** 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 247 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 161 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.5664 (OUTLIER) cc_final: 0.5171 (t-90) REVERT: A 295 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5729 (pm20) REVERT: A 714 MET cc_start: 0.8023 (ttt) cc_final: 0.7750 (ttp) REVERT: A 967 LEU cc_start: 0.7496 (tt) cc_final: 0.7133 (mm) REVERT: A 971 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: B 598 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7957 (tt) REVERT: B 948 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7912 (tm-30) REVERT: C 199 SER cc_start: 0.8673 (m) cc_final: 0.8421 (t) REVERT: C 296 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (mm) REVERT: C 519 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6592 (t0) REVERT: C 747 ASN cc_start: 0.7647 (m-40) cc_final: 0.7111 (t0) REVERT: C 837 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6422 (mptt) outliers start: 86 outliers final: 68 residues processed: 233 average time/residue: 0.1284 time to fit residues: 49.9288 Evaluate side-chains 225 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 124 LEU 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 521 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 713 SER 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 1105 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 272 THR 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 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 638 ILE 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 841 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 1012 MET 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 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 223 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 296 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 721 CYS 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 1023 VAL Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 216 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.107013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082132 restraints weight = 71010.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080892 restraints weight = 62602.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081438 restraints weight = 53277.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081781 restraints weight = 45722.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081845 restraints weight = 39678.457| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23190 Z= 0.171 Angle : 0.661 10.730 31658 Z= 0.325 Chirality : 0.047 0.416 3724 Planarity : 0.005 0.059 4024 Dihedral : 6.113 56.892 4126 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.86 % Rotamer: Outliers : 3.47 % Allowed : 22.20 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 2784 helix: 2.14 (0.21), residues: 601 sheet: -0.17 (0.22), residues: 524 loop : -1.48 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 966 TYR 0.022 0.002 TYR A 887 PHE 0.025 0.002 PHE B 162 TRP 0.065 0.003 TRP C 246 HIS 0.010 0.001 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00401 (23102) covalent geometry : angle 0.63362 (31428) SS BOND : bond 0.00343 ( 34) SS BOND : angle 1.30025 ( 68) hydrogen bonds : bond 0.04430 ( 868) hydrogen bonds : angle 5.65224 ( 2451) link_BETA1-4 : bond 0.00439 ( 19) link_BETA1-4 : angle 1.70758 ( 57) link_NAG-ASN : bond 0.00634 ( 35) link_NAG-ASN : angle 2.97155 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.76 seconds wall clock time: 53 minutes 42.47 seconds (3222.47 seconds total)