Starting phenix.real_space_refine on Thu Mar 5 11:46:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf3_25860/03_2026/7tf3_25860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf3_25860/03_2026/7tf3_25860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf3_25860/03_2026/7tf3_25860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf3_25860/03_2026/7tf3_25860.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf3_25860/03_2026/7tf3_25860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf3_25860/03_2026/7tf3_25860.cif" } resolution = 2.25 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= 0.023 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 92 5.16 5 C 13909 2.51 5 N 3583 2.21 5 O 4289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21873 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6500 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6500 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8089 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.15, per 1000 atoms: 0.24 Number of scatterers: 21873 At special positions: 0 Unit cell: (141, 147, 174, 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 92 16.00 O 4289 8.00 N 3583 7.00 C 13909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 45 sheets defined 26.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.055A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.925A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.562A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.975A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.592A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.531A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.513A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.992A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.664A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.556A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.914A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.662A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.946A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.521A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.205A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.553A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.835A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.964A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.730A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 144 removed outlier: 7.063A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.678A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.705A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.661A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.340A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.109A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.712A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.707A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.237A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.563A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.596A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.107A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.109A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.024A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.556A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.831A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.838A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.887A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.683A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.239A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.290A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2790 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: 5.36 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6619 1.34 - 1.46: 5557 1.46 - 1.58: 10054 1.58 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22346 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 22341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 29186 1.92 - 3.84: 1110 3.84 - 5.75: 89 5.75 - 7.67: 26 7.67 - 9.59: 8 Bond angle restraints: 30419 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.44 -5.74 1.22e+00 6.72e-01 2.22e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.37 -5.67 1.22e+00 6.72e-01 2.16e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.00 -5.30 1.22e+00 6.72e-01 1.89e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.36 -4.43 1.20e+00 6.94e-01 1.36e+01 ... (remaining 30414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12964 17.93 - 35.86: 870 35.86 - 53.79: 150 53.79 - 71.73: 55 71.73 - 89.66: 25 Dihedral angle restraints: 14064 sinusoidal: 6209 harmonic: 7855 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -57.50 -28.50 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 14061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2712 0.059 - 0.117: 774 0.117 - 0.175: 140 0.175 - 0.234: 23 0.234 - 0.292: 5 Chirality restraints: 3654 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3651 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.50e-02 5.61e+00 pdb=" CG TRP A 886 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C MET C 902 " 0.041 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.41e+00 pdb=" CG TRP C 886 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.003 2.00e-02 2.50e+03 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5876 2.81 - 3.33: 18476 3.33 - 3.85: 37465 3.85 - 4.38: 43155 4.38 - 4.90: 73914 Nonbonded interactions: 178886 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.329 3.040 ... (remaining 178881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.180 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 0.069 22436 Z= 0.247 Angle : 0.858 14.917 30655 Z= 0.452 Chirality : 0.057 0.292 3654 Planarity : 0.006 0.055 3860 Dihedral : 12.938 89.657 8892 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 are not related in a simple way. whole: 0.09 (0.15), residues: 2651 helix: 1.28 (0.19), residues: 607 sheet: 0.71 (0.20), residues: 582 loop : -0.74 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.035 0.003 TYR C1067 PHE 0.034 0.002 PHE A 275 TRP 0.040 0.003 TRP A 886 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00521 (22346) covalent geometry : angle 0.82346 (30419) SS BOND : bond 0.00334 ( 34) SS BOND : angle 1.29406 ( 68) hydrogen bonds : bond 0.12160 ( 958) hydrogen bonds : angle 7.34017 ( 2790) link_BETA1-4 : bond 0.00802 ( 18) link_BETA1-4 : angle 1.60192 ( 54) link_NAG-ASN : bond 0.00773 ( 38) link_NAG-ASN : angle 3.82542 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7716 (tp) cc_final: 0.7495 (mp) REVERT: A 205 SER cc_start: 0.8576 (t) cc_final: 0.8375 (m) REVERT: A 240 THR cc_start: 0.7857 (m) cc_final: 0.7220 (t) REVERT: A 697 MET cc_start: 0.8976 (ptt) cc_final: 0.8767 (ptt) REVERT: A 994 ASP cc_start: 0.8067 (t70) cc_final: 0.7837 (t0) REVERT: B 190 ARG cc_start: 0.7063 (mpt-90) cc_final: 0.6608 (mmm160) REVERT: B 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8033 (pt) REVERT: B 987 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8087 (Cg_endo) REVERT: B 1029 MET cc_start: 0.9123 (tpp) cc_final: 0.8555 (tpp) REVERT: C 269 TYR cc_start: 0.7308 (m-80) cc_final: 0.7037 (m-80) REVERT: C 270 LEU cc_start: 0.7449 (mt) cc_final: 0.6742 (mt) REVERT: C 351 TYR cc_start: 0.7831 (p90) cc_final: 0.7463 (p90) REVERT: C 378 LYS cc_start: 0.8273 (ttmt) cc_final: 0.8022 (ttpp) REVERT: C 408 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7249 (ptm160) REVERT: C 453 TYR cc_start: 0.5453 (p90) cc_final: 0.5151 (p90) REVERT: C 586 ASP cc_start: 0.7260 (t70) cc_final: 0.6987 (t0) REVERT: C 858 LEU cc_start: 0.8638 (mp) cc_final: 0.8169 (tp) REVERT: C 1029 MET cc_start: 0.9296 (tpp) cc_final: 0.9078 (tpp) outliers start: 0 outliers final: 2 residues processed: 288 average time/residue: 0.6665 time to fit residues: 216.6709 Evaluate side-chains 137 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain C residue 574 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 10.0000 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 755 GLN A 926 GLN A 954 GLN A1002 GLN A1071 HIS B 901 GLN B 955 ASN B1011 GLN C 580 GLN C 606 ASN C 954 GLN C1002 GLN C1010 GLN C1071 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.137559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085114 restraints weight = 37762.183| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.48 r_work: 0.3129 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22436 Z= 0.122 Angle : 0.570 10.422 30655 Z= 0.287 Chirality : 0.044 0.239 3654 Planarity : 0.004 0.043 3860 Dihedral : 6.843 105.280 4056 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.69 % Allowed : 7.30 % Favored : 91.01 % 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 are not related in a simple way. whole: 0.62 (0.16), residues: 2651 helix: 2.27 (0.21), residues: 616 sheet: 0.73 (0.21), residues: 607 loop : -0.56 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.027 0.001 TYR A 170 PHE 0.020 0.001 PHE C 238 TRP 0.017 0.001 TRP B 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (22346) covalent geometry : angle 0.54082 (30419) SS BOND : bond 0.00318 ( 34) SS BOND : angle 0.87160 ( 68) hydrogen bonds : bond 0.04291 ( 958) hydrogen bonds : angle 5.92198 ( 2790) link_BETA1-4 : bond 0.00224 ( 18) link_BETA1-4 : angle 1.11106 ( 54) link_NAG-ASN : bond 0.00539 ( 38) link_NAG-ASN : angle 2.88859 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7641 (tp) cc_final: 0.7279 (mp) REVERT: A 200 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.5756 (t80) REVERT: A 205 SER cc_start: 0.8781 (t) cc_final: 0.8537 (m) REVERT: A 240 THR cc_start: 0.7819 (m) cc_final: 0.7353 (t) REVERT: A 990 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: A 994 ASP cc_start: 0.8660 (t70) cc_final: 0.8452 (t0) REVERT: B 580 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6759 (mt0) REVERT: B 858 LEU cc_start: 0.8569 (mt) cc_final: 0.7889 (pt) REVERT: B 987 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7843 (Cg_endo) REVERT: B 1092 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8699 (mt-10) REVERT: C 200 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6473 (t80) REVERT: C 269 TYR cc_start: 0.7470 (m-80) cc_final: 0.6860 (m-80) REVERT: C 378 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7735 (ttpp) REVERT: C 408 ARG cc_start: 0.7703 (ptt90) cc_final: 0.7350 (ppt170) REVERT: C 436 TRP cc_start: 0.6302 (OUTLIER) cc_final: 0.5072 (p-90) REVERT: C 586 ASP cc_start: 0.7308 (t70) cc_final: 0.6783 (t0) REVERT: C 964 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8779 (mtmt) REVERT: C 987 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.8252 (Cg_endo) REVERT: C 1029 MET cc_start: 0.9479 (tpp) cc_final: 0.9204 (tpp) outliers start: 40 outliers final: 13 residues processed: 167 average time/residue: 0.5707 time to fit residues: 110.5650 Evaluate side-chains 133 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 99 ASN C1010 GLN C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.136413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083537 restraints weight = 37539.129| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.53 r_work: 0.3099 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22436 Z= 0.129 Angle : 0.551 10.306 30655 Z= 0.275 Chirality : 0.044 0.261 3654 Planarity : 0.004 0.055 3860 Dihedral : 6.026 59.409 4052 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.73 % Allowed : 8.48 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2651 helix: 2.48 (0.21), residues: 624 sheet: 0.70 (0.20), residues: 630 loop : -0.47 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 102 TYR 0.025 0.002 TYR C 170 PHE 0.017 0.001 PHE B 238 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00285 (22346) covalent geometry : angle 0.52327 (30419) SS BOND : bond 0.00123 ( 34) SS BOND : angle 0.70978 ( 68) hydrogen bonds : bond 0.04167 ( 958) hydrogen bonds : angle 5.58405 ( 2790) link_BETA1-4 : bond 0.00349 ( 18) link_BETA1-4 : angle 1.09078 ( 54) link_NAG-ASN : bond 0.00562 ( 38) link_NAG-ASN : angle 2.78598 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7656 (tp) cc_final: 0.7273 (mp) REVERT: A 200 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5949 (t80) REVERT: A 205 SER cc_start: 0.8856 (t) cc_final: 0.8612 (m) REVERT: A 240 THR cc_start: 0.7996 (m) cc_final: 0.7778 (t) REVERT: A 994 ASP cc_start: 0.8740 (t70) cc_final: 0.8490 (t0) REVERT: B 52 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8309 (tp-100) REVERT: B 571 ASP cc_start: 0.8338 (m-30) cc_final: 0.7902 (t70) REVERT: B 580 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6674 (mt0) REVERT: B 858 LEU cc_start: 0.8760 (mt) cc_final: 0.8007 (pt) REVERT: B 987 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7873 (Cg_endo) REVERT: B 1092 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8673 (mt-10) REVERT: B 1141 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7797 (tm) REVERT: C 52 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7959 (tp-100) REVERT: C 135 PHE cc_start: 0.7208 (t80) cc_final: 0.6937 (t80) REVERT: C 200 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6380 (t80) REVERT: C 269 TYR cc_start: 0.7477 (m-80) cc_final: 0.6682 (m-10) REVERT: C 309 GLU cc_start: 0.7726 (mp0) cc_final: 0.7152 (pm20) REVERT: C 378 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7736 (ttpp) REVERT: C 408 ARG cc_start: 0.7677 (ptt90) cc_final: 0.7351 (ppt170) REVERT: C 436 TRP cc_start: 0.6281 (OUTLIER) cc_final: 0.5025 (p-90) REVERT: C 505 TYR cc_start: 0.7271 (p90) cc_final: 0.7069 (p90) REVERT: C 586 ASP cc_start: 0.7256 (t70) cc_final: 0.6814 (t0) REVERT: C 740 MET cc_start: 0.9152 (tpp) cc_final: 0.8782 (ttt) REVERT: C 964 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8797 (mtmt) REVERT: C 987 PRO cc_start: 0.8577 (Cg_exo) cc_final: 0.8202 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7857 (tm-30) REVERT: C 1029 MET cc_start: 0.9462 (tpp) cc_final: 0.9213 (tpp) outliers start: 41 outliers final: 13 residues processed: 158 average time/residue: 0.5147 time to fit residues: 95.8045 Evaluate side-chains 132 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 120 optimal weight: 0.0170 chunk 143 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN A 824 ASN B 764 ASN B 824 ASN B 955 ASN C 121 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.133915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080575 restraints weight = 37397.151| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.53 r_work: 0.3046 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22436 Z= 0.196 Angle : 0.587 10.284 30655 Z= 0.294 Chirality : 0.046 0.269 3654 Planarity : 0.004 0.040 3860 Dihedral : 5.803 57.631 4052 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.90 % Allowed : 9.12 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2651 helix: 2.51 (0.21), residues: 618 sheet: 0.43 (0.20), residues: 653 loop : -0.48 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.022 0.002 TYR C1067 PHE 0.020 0.002 PHE A 275 TRP 0.018 0.002 TRP C 886 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00453 (22346) covalent geometry : angle 0.55871 (30419) SS BOND : bond 0.00172 ( 34) SS BOND : angle 0.76904 ( 68) hydrogen bonds : bond 0.04590 ( 958) hydrogen bonds : angle 5.64472 ( 2790) link_BETA1-4 : bond 0.00220 ( 18) link_BETA1-4 : angle 1.16453 ( 54) link_NAG-ASN : bond 0.00591 ( 38) link_NAG-ASN : angle 2.89990 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6134 (t80) REVERT: A 240 THR cc_start: 0.8156 (m) cc_final: 0.7918 (t) REVERT: A 324 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6548 (pm20) REVERT: A 994 ASP cc_start: 0.8781 (t70) cc_final: 0.8534 (t0) REVERT: B 269 TYR cc_start: 0.7540 (m-80) cc_final: 0.7124 (m-80) REVERT: B 271 GLN cc_start: 0.7748 (mp10) cc_final: 0.7509 (mp-120) REVERT: B 580 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6699 (mt0) REVERT: B 987 PRO cc_start: 0.8116 (Cg_exo) cc_final: 0.7806 (Cg_endo) REVERT: C 135 PHE cc_start: 0.7047 (t80) cc_final: 0.6723 (t80) REVERT: C 200 TYR cc_start: 0.6747 (t80) cc_final: 0.6522 (t80) REVERT: C 309 GLU cc_start: 0.7884 (mp0) cc_final: 0.7293 (pm20) REVERT: C 378 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7785 (ttpp) REVERT: C 436 TRP cc_start: 0.6300 (OUTLIER) cc_final: 0.4902 (p-90) REVERT: C 505 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.7053 (p90) REVERT: C 586 ASP cc_start: 0.7212 (t70) cc_final: 0.6760 (t0) REVERT: C 646 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8039 (ttp80) REVERT: C 740 MET cc_start: 0.9183 (tpp) cc_final: 0.8749 (ttt) REVERT: C 964 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8875 (mtmt) REVERT: C 987 PRO cc_start: 0.8590 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7995 (tm-30) outliers start: 45 outliers final: 19 residues processed: 150 average time/residue: 0.5140 time to fit residues: 91.1452 Evaluate side-chains 136 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 207 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 209 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN C 779 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.133568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080564 restraints weight = 37249.025| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.46 r_work: 0.3046 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22436 Z= 0.187 Angle : 0.571 10.304 30655 Z= 0.287 Chirality : 0.046 0.268 3654 Planarity : 0.004 0.039 3860 Dihedral : 5.626 59.101 4052 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.90 % Allowed : 9.84 % Favored : 88.27 % 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 are not related in a simple way. whole: 0.67 (0.16), residues: 2651 helix: 2.55 (0.21), residues: 618 sheet: 0.32 (0.20), residues: 652 loop : -0.46 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.023 0.002 TYR A 170 PHE 0.029 0.002 PHE A 238 TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00430 (22346) covalent geometry : angle 0.54266 (30419) SS BOND : bond 0.00163 ( 34) SS BOND : angle 0.71840 ( 68) hydrogen bonds : bond 0.04432 ( 958) hydrogen bonds : angle 5.58393 ( 2790) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.08123 ( 54) link_NAG-ASN : bond 0.00566 ( 38) link_NAG-ASN : angle 2.86342 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6141 (t80) REVERT: A 586 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: A 964 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8495 (mppt) REVERT: A 994 ASP cc_start: 0.8789 (t70) cc_final: 0.8542 (t0) REVERT: B 269 TYR cc_start: 0.7534 (m-80) cc_final: 0.7141 (m-80) REVERT: B 580 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6770 (mt0) REVERT: B 987 PRO cc_start: 0.8018 (Cg_exo) cc_final: 0.7776 (Cg_endo) REVERT: B 1142 GLN cc_start: 0.8376 (tp40) cc_final: 0.8019 (tm-30) REVERT: C 135 PHE cc_start: 0.7072 (t80) cc_final: 0.6833 (t80) REVERT: C 200 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6498 (t80) REVERT: C 309 GLU cc_start: 0.7936 (mp0) cc_final: 0.7340 (pm20) REVERT: C 378 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7766 (ttpp) REVERT: C 436 TRP cc_start: 0.6343 (OUTLIER) cc_final: 0.4896 (p-90) REVERT: C 505 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.7109 (p90) REVERT: C 586 ASP cc_start: 0.7239 (t70) cc_final: 0.6580 (t0) REVERT: C 646 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8012 (ttp80) REVERT: C 964 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8839 (mtmt) REVERT: C 987 PRO cc_start: 0.8615 (Cg_exo) cc_final: 0.8231 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7952 (tm-30) outliers start: 45 outliers final: 20 residues processed: 144 average time/residue: 0.5269 time to fit residues: 88.9724 Evaluate side-chains 132 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 92 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 211 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN B 580 GLN C 52 GLN C 394 ASN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.133886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081000 restraints weight = 37354.995| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.51 r_work: 0.3053 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22436 Z= 0.149 Angle : 0.549 10.376 30655 Z= 0.276 Chirality : 0.045 0.265 3654 Planarity : 0.004 0.039 3860 Dihedral : 5.432 59.400 4052 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 10.13 % Favored : 88.01 % 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 are not related in a simple way. whole: 0.71 (0.16), residues: 2651 helix: 2.62 (0.21), residues: 624 sheet: 0.33 (0.20), residues: 640 loop : -0.45 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.023 0.001 TYR A 170 PHE 0.018 0.001 PHE A 79 TRP 0.007 0.001 TRP C 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00336 (22346) covalent geometry : angle 0.52121 (30419) SS BOND : bond 0.00126 ( 34) SS BOND : angle 0.65982 ( 68) hydrogen bonds : bond 0.04213 ( 958) hydrogen bonds : angle 5.47877 ( 2790) link_BETA1-4 : bond 0.00302 ( 18) link_BETA1-4 : angle 1.04809 ( 54) link_NAG-ASN : bond 0.00550 ( 38) link_NAG-ASN : angle 2.80070 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6174 (t80) REVERT: A 586 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: A 964 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8485 (mppt) REVERT: A 994 ASP cc_start: 0.8773 (t70) cc_final: 0.8516 (t0) REVERT: B 269 TYR cc_start: 0.7485 (m-80) cc_final: 0.7130 (m-80) REVERT: B 569 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8304 (pt) REVERT: B 987 PRO cc_start: 0.8009 (Cg_exo) cc_final: 0.7779 (Cg_endo) REVERT: B 1142 GLN cc_start: 0.8382 (tp40) cc_final: 0.8038 (tm-30) REVERT: C 64 TRP cc_start: 0.6566 (t60) cc_final: 0.6098 (t-100) REVERT: C 135 PHE cc_start: 0.7016 (t80) cc_final: 0.6763 (t80) REVERT: C 309 GLU cc_start: 0.7950 (mp0) cc_final: 0.7339 (pm20) REVERT: C 378 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7766 (ttpp) REVERT: C 436 TRP cc_start: 0.6375 (OUTLIER) cc_final: 0.4999 (p-90) REVERT: C 505 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.7088 (p90) REVERT: C 531 THR cc_start: 0.8670 (m) cc_final: 0.8070 (p) REVERT: C 586 ASP cc_start: 0.7207 (t70) cc_final: 0.6624 (t0) REVERT: C 646 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7932 (ttp80) REVERT: C 740 MET cc_start: 0.9149 (tpp) cc_final: 0.8708 (ttt) REVERT: C 964 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8769 (mtmt) REVERT: C 987 PRO cc_start: 0.8538 (Cg_exo) cc_final: 0.8167 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7959 (tm-30) outliers start: 44 outliers final: 17 residues processed: 146 average time/residue: 0.5244 time to fit residues: 89.4785 Evaluate side-chains 134 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 194 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 237 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.133095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079577 restraints weight = 37503.573| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.56 r_work: 0.3031 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22436 Z= 0.180 Angle : 0.569 10.414 30655 Z= 0.287 Chirality : 0.046 0.263 3654 Planarity : 0.004 0.041 3860 Dihedral : 5.374 58.402 4052 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.73 % Allowed : 10.34 % Favored : 87.93 % 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 are not related in a simple way. whole: 0.66 (0.16), residues: 2651 helix: 2.60 (0.21), residues: 624 sheet: 0.33 (0.20), residues: 632 loop : -0.51 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.024 0.002 TYR A 170 PHE 0.029 0.002 PHE B 201 TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00414 (22346) covalent geometry : angle 0.54087 (30419) SS BOND : bond 0.00165 ( 34) SS BOND : angle 0.75799 ( 68) hydrogen bonds : bond 0.04381 ( 958) hydrogen bonds : angle 5.51717 ( 2790) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.08611 ( 54) link_NAG-ASN : bond 0.00565 ( 38) link_NAG-ASN : angle 2.85582 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6203 (t80) REVERT: A 569 ILE cc_start: 0.8629 (mp) cc_final: 0.8403 (pt) REVERT: A 586 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: A 964 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8361 (mttt) REVERT: A 994 ASP cc_start: 0.8789 (t70) cc_final: 0.8536 (t0) REVERT: B 269 TYR cc_start: 0.7528 (m-80) cc_final: 0.7079 (m-80) REVERT: B 271 GLN cc_start: 0.7821 (mp10) cc_final: 0.7603 (mp-120) REVERT: B 569 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (pt) REVERT: B 987 PRO cc_start: 0.8037 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: B 1142 GLN cc_start: 0.8380 (tp40) cc_final: 0.8056 (tm-30) REVERT: C 64 TRP cc_start: 0.6585 (t60) cc_final: 0.6086 (t-100) REVERT: C 135 PHE cc_start: 0.6978 (t80) cc_final: 0.6687 (t80) REVERT: C 278 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7850 (tttt) REVERT: C 309 GLU cc_start: 0.7977 (mp0) cc_final: 0.7340 (pm20) REVERT: C 320 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7730 (m) REVERT: C 378 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7800 (ttpp) REVERT: C 421 TYR cc_start: 0.8057 (m-10) cc_final: 0.7428 (m-10) REVERT: C 436 TRP cc_start: 0.6409 (OUTLIER) cc_final: 0.5029 (p-90) REVERT: C 505 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.7073 (p90) REVERT: C 531 THR cc_start: 0.8677 (m) cc_final: 0.8105 (p) REVERT: C 586 ASP cc_start: 0.7160 (t70) cc_final: 0.6586 (t0) REVERT: C 619 GLU cc_start: 0.7533 (mp0) cc_final: 0.7260 (mp0) REVERT: C 646 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: C 740 MET cc_start: 0.9136 (tpp) cc_final: 0.8687 (ttt) REVERT: C 964 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8782 (ttmt) REVERT: C 987 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8086 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7938 (tm-30) outliers start: 41 outliers final: 18 residues processed: 151 average time/residue: 0.5126 time to fit residues: 91.3265 Evaluate side-chains 141 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 175 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN C1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.133520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080233 restraints weight = 37199.274| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.55 r_work: 0.3047 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22436 Z= 0.145 Angle : 0.543 10.590 30655 Z= 0.273 Chirality : 0.045 0.264 3654 Planarity : 0.004 0.042 3860 Dihedral : 5.212 55.924 4052 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.44 % Allowed : 10.93 % Favored : 87.63 % 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 are not related in a simple way. whole: 0.71 (0.16), residues: 2651 helix: 2.71 (0.21), residues: 624 sheet: 0.33 (0.20), residues: 650 loop : -0.50 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.024 0.001 TYR A 170 PHE 0.018 0.001 PHE A 79 TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00330 (22346) covalent geometry : angle 0.51476 (30419) SS BOND : bond 0.00124 ( 34) SS BOND : angle 0.67768 ( 68) hydrogen bonds : bond 0.04107 ( 958) hydrogen bonds : angle 5.39074 ( 2790) link_BETA1-4 : bond 0.00313 ( 18) link_BETA1-4 : angle 1.01367 ( 54) link_NAG-ASN : bond 0.00536 ( 38) link_NAG-ASN : angle 2.77155 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7726 (tp) cc_final: 0.7194 (mt) REVERT: A 200 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6272 (t80) REVERT: A 569 ILE cc_start: 0.8647 (mp) cc_final: 0.8420 (pt) REVERT: A 586 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: A 964 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8483 (mppt) REVERT: A 994 ASP cc_start: 0.8770 (t70) cc_final: 0.8523 (t0) REVERT: B 189 LEU cc_start: 0.7595 (mt) cc_final: 0.7249 (mt) REVERT: B 190 ARG cc_start: 0.6852 (mpt-90) cc_final: 0.6469 (mmm160) REVERT: B 269 TYR cc_start: 0.7497 (m-80) cc_final: 0.7103 (m-80) REVERT: B 569 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8367 (pt) REVERT: B 1142 GLN cc_start: 0.8378 (tp40) cc_final: 0.8068 (tm-30) REVERT: C 53 ASP cc_start: 0.7063 (t70) cc_final: 0.6840 (t0) REVERT: C 64 TRP cc_start: 0.6562 (t60) cc_final: 0.6065 (t-100) REVERT: C 135 PHE cc_start: 0.6962 (t80) cc_final: 0.6680 (t80) REVERT: C 309 GLU cc_start: 0.7950 (mp0) cc_final: 0.7325 (pm20) REVERT: C 378 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7752 (ttpp) REVERT: C 421 TYR cc_start: 0.8076 (m-10) cc_final: 0.7413 (m-10) REVERT: C 436 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.5166 (p-90) REVERT: C 505 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.7079 (p90) REVERT: C 531 THR cc_start: 0.8699 (m) cc_final: 0.8146 (p) REVERT: C 586 ASP cc_start: 0.7101 (t70) cc_final: 0.6554 (t0) REVERT: C 619 GLU cc_start: 0.7555 (mp0) cc_final: 0.7265 (mp0) REVERT: C 646 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7957 (ttp80) REVERT: C 740 MET cc_start: 0.9114 (tpp) cc_final: 0.8670 (ttt) REVERT: C 820 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: C 964 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (ttmt) REVERT: C 987 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.8101 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7976 (tm-30) outliers start: 34 outliers final: 16 residues processed: 142 average time/residue: 0.5196 time to fit residues: 86.8875 Evaluate side-chains 139 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 166 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A1142 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079626 restraints weight = 37330.361| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.55 r_work: 0.3037 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22436 Z= 0.175 Angle : 0.562 10.568 30655 Z= 0.283 Chirality : 0.045 0.265 3654 Planarity : 0.004 0.041 3860 Dihedral : 5.228 53.501 4052 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.44 % Allowed : 11.31 % Favored : 87.25 % 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 are not related in a simple way. whole: 0.66 (0.16), residues: 2651 helix: 2.68 (0.21), residues: 617 sheet: 0.30 (0.20), residues: 640 loop : -0.51 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.024 0.002 TYR A 170 PHE 0.030 0.002 PHE B 201 TRP 0.006 0.001 TRP C 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00403 (22346) covalent geometry : angle 0.53446 (30419) SS BOND : bond 0.00144 ( 34) SS BOND : angle 0.71130 ( 68) hydrogen bonds : bond 0.04269 ( 958) hydrogen bonds : angle 5.44257 ( 2790) link_BETA1-4 : bond 0.00268 ( 18) link_BETA1-4 : angle 1.05734 ( 54) link_NAG-ASN : bond 0.00549 ( 38) link_NAG-ASN : angle 2.81290 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7700 (tp) cc_final: 0.7231 (mt) REVERT: A 200 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6249 (t80) REVERT: A 569 ILE cc_start: 0.8643 (mp) cc_final: 0.8403 (pt) REVERT: A 586 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6753 (m-30) REVERT: A 994 ASP cc_start: 0.8795 (t70) cc_final: 0.8537 (t0) REVERT: B 189 LEU cc_start: 0.7658 (mt) cc_final: 0.7309 (mt) REVERT: B 190 ARG cc_start: 0.6940 (mpt-90) cc_final: 0.6538 (mmm160) REVERT: B 269 TYR cc_start: 0.7526 (m-80) cc_final: 0.7136 (m-80) REVERT: B 569 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8449 (pt) REVERT: B 1142 GLN cc_start: 0.8373 (tp40) cc_final: 0.8053 (tm-30) REVERT: C 53 ASP cc_start: 0.7082 (t70) cc_final: 0.6876 (t0) REVERT: C 64 TRP cc_start: 0.6544 (t60) cc_final: 0.6085 (t-100) REVERT: C 135 PHE cc_start: 0.6909 (t80) cc_final: 0.6679 (t80) REVERT: C 278 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7885 (tttt) REVERT: C 309 GLU cc_start: 0.7955 (mp0) cc_final: 0.7373 (pm20) REVERT: C 378 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7806 (ttpp) REVERT: C 421 TYR cc_start: 0.8132 (m-10) cc_final: 0.7514 (m-10) REVERT: C 436 TRP cc_start: 0.6399 (OUTLIER) cc_final: 0.5260 (p-90) REVERT: C 505 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.7070 (p90) REVERT: C 531 THR cc_start: 0.8713 (m) cc_final: 0.8153 (p) REVERT: C 586 ASP cc_start: 0.7046 (t70) cc_final: 0.6552 (t0) REVERT: C 619 GLU cc_start: 0.7568 (mp0) cc_final: 0.7269 (mp0) REVERT: C 646 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7971 (ttp80) REVERT: C 740 MET cc_start: 0.9121 (tpp) cc_final: 0.8690 (ttt) REVERT: C 820 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: C 964 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8822 (ttmt) REVERT: C 987 PRO cc_start: 0.8476 (Cg_exo) cc_final: 0.8096 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7943 (tm-30) outliers start: 34 outliers final: 18 residues processed: 141 average time/residue: 0.5257 time to fit residues: 87.4674 Evaluate side-chains 140 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 201 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** C1010 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.133001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079671 restraints weight = 37394.002| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.55 r_work: 0.3036 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22436 Z= 0.170 Angle : 0.564 10.644 30655 Z= 0.284 Chirality : 0.045 0.265 3654 Planarity : 0.004 0.042 3860 Dihedral : 5.223 52.833 4052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.18 % Allowed : 11.57 % Favored : 87.25 % 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 are not related in a simple way. whole: 0.66 (0.16), residues: 2651 helix: 2.69 (0.21), residues: 617 sheet: 0.26 (0.20), residues: 650 loop : -0.51 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.025 0.002 TYR A 170 PHE 0.029 0.001 PHE A 238 TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00390 (22346) covalent geometry : angle 0.53677 (30419) SS BOND : bond 0.00134 ( 34) SS BOND : angle 0.70734 ( 68) hydrogen bonds : bond 0.04253 ( 958) hydrogen bonds : angle 5.44223 ( 2790) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.04860 ( 54) link_NAG-ASN : bond 0.00547 ( 38) link_NAG-ASN : angle 2.82318 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7684 (tp) cc_final: 0.7222 (mt) REVERT: A 200 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6288 (t80) REVERT: A 569 ILE cc_start: 0.8641 (mp) cc_final: 0.8404 (pt) REVERT: A 586 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: A 994 ASP cc_start: 0.8784 (t70) cc_final: 0.8525 (t0) REVERT: B 189 LEU cc_start: 0.7686 (mt) cc_final: 0.7357 (mt) REVERT: B 190 ARG cc_start: 0.6905 (mpt-90) cc_final: 0.6512 (mmm160) REVERT: B 269 TYR cc_start: 0.7511 (m-80) cc_final: 0.7103 (m-80) REVERT: B 1142 GLN cc_start: 0.8383 (tp40) cc_final: 0.8082 (tm-30) REVERT: C 53 ASP cc_start: 0.7080 (t70) cc_final: 0.6836 (t0) REVERT: C 64 TRP cc_start: 0.6498 (t60) cc_final: 0.6047 (t-100) REVERT: C 135 PHE cc_start: 0.6860 (t80) cc_final: 0.6616 (t80) REVERT: C 278 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7848 (tttt) REVERT: C 309 GLU cc_start: 0.7952 (mp0) cc_final: 0.7372 (pm20) REVERT: C 378 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7771 (ttpp) REVERT: C 421 TYR cc_start: 0.8140 (m-10) cc_final: 0.7456 (m-10) REVERT: C 436 TRP cc_start: 0.6362 (OUTLIER) cc_final: 0.5327 (p-90) REVERT: C 455 LEU cc_start: 0.6501 (tt) cc_final: 0.6266 (tt) REVERT: C 505 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.7066 (p90) REVERT: C 516 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: C 531 THR cc_start: 0.8719 (m) cc_final: 0.8164 (p) REVERT: C 586 ASP cc_start: 0.7058 (t70) cc_final: 0.6565 (t0) REVERT: C 619 GLU cc_start: 0.7579 (mp0) cc_final: 0.7261 (mp0) REVERT: C 646 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: C 740 MET cc_start: 0.9116 (tpp) cc_final: 0.8683 (ttt) REVERT: C 820 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: C 964 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8813 (ttmt) REVERT: C 987 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8112 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7951 (tm-30) outliers start: 28 outliers final: 18 residues processed: 137 average time/residue: 0.5446 time to fit residues: 87.7038 Evaluate side-chains 141 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 171 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 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 = 0.4070 r_free = 0.4070 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079711 restraints weight = 37369.293| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.55 r_work: 0.3034 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22436 Z= 0.170 Angle : 0.565 11.082 30655 Z= 0.285 Chirality : 0.045 0.265 3654 Planarity : 0.004 0.042 3860 Dihedral : 5.217 52.207 4052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.31 % Allowed : 11.65 % Favored : 87.04 % 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 are not related in a simple way. whole: 0.66 (0.16), residues: 2651 helix: 2.68 (0.21), residues: 617 sheet: 0.26 (0.20), residues: 640 loop : -0.51 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.025 0.002 TYR A 170 PHE 0.031 0.001 PHE B 201 TRP 0.006 0.001 TRP C 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00390 (22346) covalent geometry : angle 0.53735 (30419) SS BOND : bond 0.00133 ( 34) SS BOND : angle 0.70556 ( 68) hydrogen bonds : bond 0.04247 ( 958) hydrogen bonds : angle 5.43412 ( 2790) link_BETA1-4 : bond 0.00293 ( 18) link_BETA1-4 : angle 1.04868 ( 54) link_NAG-ASN : bond 0.00544 ( 38) link_NAG-ASN : angle 2.82437 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13018.45 seconds wall clock time: 220 minutes 41.16 seconds (13241.16 seconds total)