Starting phenix.real_space_refine on Thu Mar 5 11:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tey_25855/03_2026/7tey_25855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tey_25855/03_2026/7tey_25855.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/7tey_25855/03_2026/7tey_25855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tey_25855/03_2026/7tey_25855.map" model { file = "/net/cci-nas-00/data/ceres_data/7tey_25855/03_2026/7tey_25855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tey_25855/03_2026/7tey_25855.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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 13904 2.51 5 N 3584 2.21 5 O 4287 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: 21867 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8091 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: 4.90, per 1000 atoms: 0.22 Number of scatterers: 21867 At special positions: 0 Unit cell: (140, 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 4287 8.00 N 3584 7.00 C 13904 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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: 1.70 Conformation dependent library (CDL) restraints added in 969.9 milliseconds 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: 5064 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 44 sheets defined 26.1% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.052A 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: 3.700A 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: 3.913A 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: 3.564A 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: 4.062A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.595A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.952A 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: 3.615A 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 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.910A 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: 3.539A 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: 4.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.533A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.897A 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 389 removed outlier: 3.646A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.564A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.892A 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: 3.656A 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: 3.956A 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: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 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: 7.897A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.829A 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: 3.568A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.259A 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: 3.963A 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: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.396A 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: 7.067A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.889A 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: 6.650A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.006A 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: 5.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.506A 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: 6.051A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.314A 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: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.800A 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: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.941A 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: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A 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: 4.283A 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: 3.660A 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: 8.324A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.114A 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: 3.741A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.713A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.674A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.560A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.146A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.021A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.452A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.857A 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: 6.913A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.205A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.574A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2793 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: 4.79 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6755 1.34 - 1.46: 5506 1.46 - 1.59: 9960 1.59 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22337 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 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 6.90e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 ... (remaining 22332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 29139 1.89 - 3.77: 1124 3.77 - 5.66: 99 5.66 - 7.54: 32 7.54 - 9.43: 7 Bond angle restraints: 30401 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 110.70 116.38 -5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.09 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.42 -4.49 1.20e+00 6.94e-01 1.40e+01 ... (remaining 30396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12970 17.92 - 35.84: 867 35.84 - 53.76: 146 53.76 - 71.68: 56 71.68 - 89.60: 25 Dihedral angle restraints: 14064 sinusoidal: 6215 harmonic: 7849 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 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+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 -58.25 -27.75 1 1.00e+01 1.00e-02 1.10e+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 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 14061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3072 0.081 - 0.163: 539 0.163 - 0.244: 33 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 3647 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+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 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 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 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3644 not shown) Planarity restraints: 3899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.016 2.00e-02 2.50e+03 1.63e-02 6.63e+00 pdb=" CG TRP C 886 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.022 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 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 886 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.021 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 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C VAL C 551 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.014 2.00e-02 2.50e+03 ... (remaining 3896 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6022 2.81 - 3.34: 18440 3.34 - 3.86: 37594 3.86 - 4.38: 43056 4.38 - 4.90: 73807 Nonbonded interactions: 178919 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.303 3.040 ... (remaining 178914 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: 5.280 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.460 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.068 22427 Z= 0.247 Angle : 0.851 15.349 30637 Z= 0.449 Chirality : 0.057 0.407 3647 Planarity : 0.006 0.054 3861 Dihedral : 12.951 89.598 8898 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.06 (0.15), residues: 2651 helix: 1.22 (0.19), residues: 612 sheet: 0.75 (0.20), residues: 581 loop : -0.78 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.036 0.003 TYR C1067 PHE 0.036 0.002 PHE A 275 TRP 0.043 0.003 TRP C 886 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00522 (22337) covalent geometry : angle 0.81934 (30401) SS BOND : bond 0.00288 ( 34) SS BOND : angle 1.21401 ( 68) hydrogen bonds : bond 0.11897 ( 953) hydrogen bonds : angle 7.35085 ( 2793) link_BETA1-4 : bond 0.00683 ( 18) link_BETA1-4 : angle 1.57074 ( 54) link_NAG-ASN : bond 0.00788 ( 38) link_NAG-ASN : angle 3.69572 ( 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 310 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7771 (tp-100) REVERT: A 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8216 (m-30) REVERT: A 205 SER cc_start: 0.8476 (t) cc_final: 0.8241 (m) REVERT: A 591 SER cc_start: 0.8322 (m) cc_final: 0.7938 (p) REVERT: B 54 LEU cc_start: 0.7467 (mm) cc_final: 0.7187 (mp) REVERT: B 287 ASP cc_start: 0.7968 (t0) cc_final: 0.7667 (m-30) REVERT: B 553 THR cc_start: 0.6995 (p) cc_final: 0.6781 (p) REVERT: B 592 PHE cc_start: 0.7294 (p90) cc_final: 0.6884 (p90) REVERT: B 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8886 (tpp) REVERT: C 129 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6218 (mmtm) REVERT: C 347 PHE cc_start: 0.6661 (m-10) cc_final: 0.6396 (m-10) REVERT: C 396 TYR cc_start: 0.6830 (m-80) cc_final: 0.6576 (m-80) REVERT: C 421 TYR cc_start: 0.8323 (m-10) cc_final: 0.8022 (m-10) REVERT: C 436 TRP cc_start: 0.7005 (p90) cc_final: 0.6577 (p90) REVERT: C 437 ASN cc_start: 0.6398 (t0) cc_final: 0.6174 (m-40) REVERT: C 453 TYR cc_start: 0.7156 (p90) cc_final: 0.6633 (p90) REVERT: C 508 TYR cc_start: 0.7844 (m-80) cc_final: 0.7041 (m-80) outliers start: 0 outliers final: 2 residues processed: 310 average time/residue: 0.6235 time to fit residues: 221.2581 Evaluate side-chains 156 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain C residue 40 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 901 GLN B 955 ASN B1002 GLN B1011 GLN C 321 GLN C 556 ASN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.152807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089367 restraints weight = 33787.308| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.53 r_work: 0.3077 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22427 Z= 0.205 Angle : 0.637 19.391 30637 Z= 0.316 Chirality : 0.047 0.370 3647 Planarity : 0.005 0.045 3861 Dihedral : 6.411 57.432 4056 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.56 % Allowed : 7.22 % Favored : 91.21 % 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: 0.48 (0.15), residues: 2651 helix: 2.05 (0.20), residues: 621 sheet: 0.70 (0.20), residues: 618 loop : -0.65 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.025 0.002 TYR C1067 PHE 0.024 0.002 PHE C 238 TRP 0.022 0.002 TRP C 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00466 (22337) covalent geometry : angle 0.58989 (30401) SS BOND : bond 0.00242 ( 34) SS BOND : angle 0.80738 ( 68) hydrogen bonds : bond 0.04899 ( 953) hydrogen bonds : angle 5.99802 ( 2793) link_BETA1-4 : bond 0.00284 ( 18) link_BETA1-4 : angle 1.17204 ( 54) link_NAG-ASN : bond 0.00686 ( 38) link_NAG-ASN : angle 3.89366 ( 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 216 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 88 ASP cc_start: 0.8639 (m-30) cc_final: 0.8423 (m-30) REVERT: A 200 TYR cc_start: 0.7736 (m-80) cc_final: 0.7262 (t80) REVERT: A 205 SER cc_start: 0.8794 (t) cc_final: 0.8503 (m) REVERT: A 569 ILE cc_start: 0.8691 (mp) cc_final: 0.8441 (tp) REVERT: A 591 SER cc_start: 0.8669 (m) cc_final: 0.7725 (p) REVERT: A 868 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: A 1010 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8382 (mp10) REVERT: B 565 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6615 (p90) REVERT: C 129 LYS cc_start: 0.6868 (mtmt) cc_final: 0.6246 (mmtt) REVERT: C 347 PHE cc_start: 0.6637 (m-10) cc_final: 0.6295 (m-10) REVERT: C 421 TYR cc_start: 0.8141 (m-10) cc_final: 0.7883 (m-10) REVERT: C 434 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5960 (mt) REVERT: C 436 TRP cc_start: 0.6580 (p90) cc_final: 0.5756 (p90) REVERT: C 508 TYR cc_start: 0.7533 (m-80) cc_final: 0.7118 (m-80) REVERT: C 740 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8028 (ttt) outliers start: 37 outliers final: 12 residues processed: 197 average time/residue: 0.5291 time to fit residues: 121.3296 Evaluate side-chains 167 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 239 GLN A 762 GLN B1002 GLN C 121 ASN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.153074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090226 restraints weight = 33711.153| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.50 r_work: 0.3089 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22427 Z= 0.140 Angle : 0.578 16.955 30637 Z= 0.284 Chirality : 0.046 0.441 3647 Planarity : 0.004 0.042 3861 Dihedral : 5.792 56.980 4052 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.73 % Allowed : 8.70 % Favored : 89.56 % 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: 0.76 (0.16), residues: 2651 helix: 2.49 (0.20), residues: 621 sheet: 0.76 (0.20), residues: 621 loop : -0.54 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.029 0.001 TYR A 170 PHE 0.027 0.001 PHE C 238 TRP 0.013 0.001 TRP C 104 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (22337) covalent geometry : angle 0.53301 (30401) SS BOND : bond 0.00115 ( 34) SS BOND : angle 0.64120 ( 68) hydrogen bonds : bond 0.04387 ( 953) hydrogen bonds : angle 5.69887 ( 2793) link_BETA1-4 : bond 0.00311 ( 18) link_BETA1-4 : angle 1.11287 ( 54) link_NAG-ASN : bond 0.00809 ( 38) link_NAG-ASN : angle 3.64806 ( 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 193 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 200 TYR cc_start: 0.7696 (m-80) cc_final: 0.7266 (t80) REVERT: A 205 SER cc_start: 0.8800 (t) cc_final: 0.8537 (m) REVERT: A 569 ILE cc_start: 0.8673 (mp) cc_final: 0.8402 (tp) REVERT: A 591 SER cc_start: 0.8838 (m) cc_final: 0.8589 (p) REVERT: A 868 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: B 565 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6801 (p90) REVERT: C 129 LYS cc_start: 0.6929 (mtmt) cc_final: 0.6284 (mmtt) REVERT: C 421 TYR cc_start: 0.8127 (m-10) cc_final: 0.7854 (m-10) REVERT: C 434 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.5978 (mt) REVERT: C 436 TRP cc_start: 0.6438 (p90) cc_final: 0.5967 (p90) REVERT: C 619 GLU cc_start: 0.7836 (mp0) cc_final: 0.7628 (mp0) REVERT: C 740 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8066 (ttt) REVERT: C 1141 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7351 (tm) outliers start: 41 outliers final: 18 residues processed: 182 average time/residue: 0.4555 time to fit residues: 99.3872 Evaluate side-chains 169 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 3 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN A 824 ASN B 245 HIS B 824 ASN B1002 GLN C 779 GLN C 824 ASN C 978 ASN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087221 restraints weight = 33792.027| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.52 r_work: 0.3041 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22427 Z= 0.235 Angle : 0.615 12.773 30637 Z= 0.305 Chirality : 0.048 0.354 3647 Planarity : 0.004 0.042 3861 Dihedral : 5.706 53.793 4052 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.73 % Allowed : 9.21 % Favored : 89.06 % 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: 0.58 (0.16), residues: 2651 helix: 2.37 (0.20), residues: 629 sheet: 0.48 (0.21), residues: 601 loop : -0.57 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.023 0.002 TYR A1067 PHE 0.027 0.002 PHE C 238 TRP 0.013 0.002 TRP C 104 HIS 0.021 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00540 (22337) covalent geometry : angle 0.57722 (30401) SS BOND : bond 0.00231 ( 34) SS BOND : angle 0.71047 ( 68) hydrogen bonds : bond 0.04872 ( 953) hydrogen bonds : angle 5.77463 ( 2793) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 1.23839 ( 54) link_NAG-ASN : bond 0.00752 ( 38) link_NAG-ASN : angle 3.41143 ( 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 192 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 200 TYR cc_start: 0.7772 (m-80) cc_final: 0.7254 (t80) REVERT: A 569 ILE cc_start: 0.8634 (mp) cc_final: 0.8322 (tp) REVERT: A 577 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5309 (ptp-110) REVERT: A 591 SER cc_start: 0.8836 (m) cc_final: 0.8462 (p) REVERT: A 858 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8795 (mt) REVERT: A 868 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: B 560 LEU cc_start: 0.8459 (mp) cc_final: 0.8176 (mp) REVERT: B 565 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6930 (p90) REVERT: B 983 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7483 (mtp180) REVERT: C 129 LYS cc_start: 0.6921 (mtmt) cc_final: 0.6302 (mmtt) REVERT: C 421 TYR cc_start: 0.8122 (m-10) cc_final: 0.7917 (m-10) REVERT: C 434 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5956 (mt) REVERT: C 436 TRP cc_start: 0.6835 (p90) cc_final: 0.6122 (p90) REVERT: C 509 ARG cc_start: 0.5552 (mtt180) cc_final: 0.5273 (ttt180) REVERT: C 740 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8051 (ttt) outliers start: 41 outliers final: 22 residues processed: 182 average time/residue: 0.4541 time to fit residues: 98.3227 Evaluate side-chains 166 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 153 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN A 955 ASN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.152423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089452 restraints weight = 33656.184| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.54 r_work: 0.3079 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22427 Z= 0.121 Angle : 0.548 11.640 30637 Z= 0.272 Chirality : 0.045 0.341 3647 Planarity : 0.004 0.039 3861 Dihedral : 5.259 53.468 4052 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.77 % Allowed : 9.67 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2651 helix: 2.68 (0.21), residues: 616 sheet: 0.57 (0.21), residues: 583 loop : -0.46 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.021 0.001 TYR C1067 PHE 0.029 0.001 PHE C 238 TRP 0.017 0.001 TRP C 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00262 (22337) covalent geometry : angle 0.51591 (30401) SS BOND : bond 0.00098 ( 34) SS BOND : angle 0.57907 ( 68) hydrogen bonds : bond 0.04142 ( 953) hydrogen bonds : angle 5.51892 ( 2793) link_BETA1-4 : bond 0.00324 ( 18) link_BETA1-4 : angle 1.06867 ( 54) link_NAG-ASN : bond 0.00678 ( 38) link_NAG-ASN : angle 3.00948 ( 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 188 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 200 TYR cc_start: 0.7716 (m-80) cc_final: 0.7254 (t80) REVERT: A 569 ILE cc_start: 0.8691 (mp) cc_final: 0.8364 (tp) REVERT: A 591 SER cc_start: 0.8870 (m) cc_final: 0.8455 (p) REVERT: A 858 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8814 (mt) REVERT: A 868 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: B 565 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7041 (p90) REVERT: B 983 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7474 (mtm-85) REVERT: C 129 LYS cc_start: 0.6829 (mtmt) cc_final: 0.6161 (mmtt) REVERT: C 238 PHE cc_start: 0.6132 (p90) cc_final: 0.4950 (p90) REVERT: C 269 TYR cc_start: 0.7244 (m-80) cc_final: 0.6931 (m-80) REVERT: C 421 TYR cc_start: 0.8146 (m-10) cc_final: 0.7797 (m-10) REVERT: C 434 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6150 (mt) REVERT: C 529 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8669 (mmtt) REVERT: C 740 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8028 (ttt) outliers start: 42 outliers final: 19 residues processed: 174 average time/residue: 0.4679 time to fit residues: 97.2298 Evaluate side-chains 162 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 191 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 0.0040 chunk 92 optimal weight: 10.0000 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 81 ASN A 762 GLN B 955 ASN B1002 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087588 restraints weight = 33630.267| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.53 r_work: 0.3046 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22427 Z= 0.188 Angle : 0.581 10.528 30637 Z= 0.290 Chirality : 0.046 0.334 3647 Planarity : 0.004 0.041 3861 Dihedral : 5.162 53.844 4052 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.90 % Allowed : 9.97 % Favored : 88.13 % 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: 0.58 (0.16), residues: 2651 helix: 2.51 (0.21), residues: 624 sheet: 0.24 (0.21), residues: 604 loop : -0.50 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.001 PHE A 168 TRP 0.019 0.001 TRP C 104 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00430 (22337) covalent geometry : angle 0.55245 (30401) SS BOND : bond 0.00163 ( 34) SS BOND : angle 0.60024 ( 68) hydrogen bonds : bond 0.04600 ( 953) hydrogen bonds : angle 5.60091 ( 2793) link_BETA1-4 : bond 0.00268 ( 18) link_BETA1-4 : angle 1.17444 ( 54) link_NAG-ASN : bond 0.00674 ( 38) link_NAG-ASN : angle 2.92379 ( 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 194 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 200 TYR cc_start: 0.7685 (m-80) cc_final: 0.7007 (t80) REVERT: A 569 ILE cc_start: 0.8614 (mp) cc_final: 0.8238 (tp) REVERT: A 591 SER cc_start: 0.8827 (m) cc_final: 0.8444 (p) REVERT: A 821 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 858 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8759 (mt) REVERT: A 868 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: B 565 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.7069 (p90) REVERT: B 983 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7537 (mtm-85) REVERT: C 52 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 129 LYS cc_start: 0.6845 (mtmt) cc_final: 0.6246 (mmtt) REVERT: C 238 PHE cc_start: 0.6144 (p90) cc_final: 0.4885 (p90) REVERT: C 269 TYR cc_start: 0.7323 (m-80) cc_final: 0.7096 (m-80) REVERT: C 421 TYR cc_start: 0.8058 (m-10) cc_final: 0.7656 (m-10) REVERT: C 516 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6542 (pp20) REVERT: C 740 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8027 (ttt) REVERT: C 1141 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7328 (tm) outliers start: 45 outliers final: 21 residues processed: 183 average time/residue: 0.4623 time to fit residues: 100.9216 Evaluate side-chains 166 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 247 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 141 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 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 66 HIS A 762 GLN B1002 GLN C 115 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088714 restraints weight = 33540.118| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.49 r_work: 0.3062 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22427 Z= 0.147 Angle : 0.554 11.716 30637 Z= 0.276 Chirality : 0.045 0.328 3647 Planarity : 0.004 0.045 3861 Dihedral : 4.971 53.684 4052 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.48 % Allowed : 10.56 % Favored : 87.96 % 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: 0.65 (0.16), residues: 2651 helix: 2.52 (0.21), residues: 629 sheet: 0.33 (0.21), residues: 579 loop : -0.46 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.021 0.001 TYR A1067 PHE 0.022 0.001 PHE C 238 TRP 0.023 0.001 TRP C 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00330 (22337) covalent geometry : angle 0.52625 (30401) SS BOND : bond 0.00103 ( 34) SS BOND : angle 0.55548 ( 68) hydrogen bonds : bond 0.04246 ( 953) hydrogen bonds : angle 5.50935 ( 2793) link_BETA1-4 : bond 0.00299 ( 18) link_BETA1-4 : angle 1.07144 ( 54) link_NAG-ASN : bond 0.00631 ( 38) link_NAG-ASN : angle 2.80762 ( 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 186 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 81 ASN cc_start: 0.6355 (OUTLIER) cc_final: 0.5859 (m110) REVERT: A 200 TYR cc_start: 0.7716 (m-80) cc_final: 0.7020 (t80) REVERT: A 221 SER cc_start: 0.8701 (t) cc_final: 0.8300 (p) REVERT: A 231 ILE cc_start: 0.8703 (pt) cc_final: 0.8454 (pp) REVERT: A 569 ILE cc_start: 0.8605 (mp) cc_final: 0.8216 (tp) REVERT: A 577 ARG cc_start: 0.5416 (OUTLIER) cc_final: 0.5163 (ptp-110) REVERT: A 591 SER cc_start: 0.8804 (m) cc_final: 0.8357 (p) REVERT: A 821 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8036 (tt) REVERT: A 858 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8787 (mt) REVERT: A 868 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: B 565 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7112 (p90) REVERT: B 983 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7538 (mtm-85) REVERT: C 52 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 129 LYS cc_start: 0.6739 (mtmt) cc_final: 0.6176 (mmtt) REVERT: C 238 PHE cc_start: 0.6041 (p90) cc_final: 0.4816 (p90) REVERT: C 269 TYR cc_start: 0.7351 (m-80) cc_final: 0.7046 (m-80) REVERT: C 421 TYR cc_start: 0.8059 (m-10) cc_final: 0.7728 (m-10) REVERT: C 532 ASN cc_start: 0.8976 (m-40) cc_final: 0.8687 (t0) REVERT: C 740 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8024 (ttt) outliers start: 35 outliers final: 22 residues processed: 179 average time/residue: 0.4516 time to fit residues: 97.0693 Evaluate side-chains 167 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 49 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 153 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 762 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.151705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089500 restraints weight = 33256.924| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.41 r_work: 0.3074 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22427 Z= 0.119 Angle : 0.534 10.056 30637 Z= 0.265 Chirality : 0.045 0.323 3647 Planarity : 0.004 0.047 3861 Dihedral : 4.719 53.761 4052 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.52 % Allowed : 10.77 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 2651 helix: 2.66 (0.21), residues: 628 sheet: 0.31 (0.21), residues: 572 loop : -0.42 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.025 0.001 TYR B 170 PHE 0.022 0.001 PHE A 168 TRP 0.031 0.001 TRP C 436 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00262 (22337) covalent geometry : angle 0.50690 (30401) SS BOND : bond 0.00086 ( 34) SS BOND : angle 0.57816 ( 68) hydrogen bonds : bond 0.03963 ( 953) hydrogen bonds : angle 5.35098 ( 2793) link_BETA1-4 : bond 0.00323 ( 18) link_BETA1-4 : angle 1.04678 ( 54) link_NAG-ASN : bond 0.00597 ( 38) link_NAG-ASN : angle 2.69457 ( 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 193 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 81 ASN cc_start: 0.6299 (OUTLIER) cc_final: 0.5767 (m110) REVERT: A 200 TYR cc_start: 0.7649 (m-80) cc_final: 0.6941 (t80) REVERT: A 221 SER cc_start: 0.8688 (t) cc_final: 0.8308 (p) REVERT: A 231 ILE cc_start: 0.8729 (pt) cc_final: 0.8483 (pp) REVERT: A 569 ILE cc_start: 0.8596 (mp) cc_final: 0.8194 (tp) REVERT: A 577 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.5077 (ptp-110) REVERT: A 591 SER cc_start: 0.8900 (m) cc_final: 0.8460 (p) REVERT: A 773 GLU cc_start: 0.8869 (tt0) cc_final: 0.8587 (tt0) REVERT: A 821 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 858 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8778 (mt) REVERT: A 868 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: B 565 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7207 (p90) REVERT: B 983 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7563 (mtm-85) REVERT: C 52 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8621 (tm-30) REVERT: C 129 LYS cc_start: 0.6720 (mtmt) cc_final: 0.6151 (mmtt) REVERT: C 238 PHE cc_start: 0.5936 (p90) cc_final: 0.4718 (p90) REVERT: C 269 TYR cc_start: 0.7326 (m-80) cc_final: 0.7102 (m-80) REVERT: C 353 TRP cc_start: 0.6990 (p-90) cc_final: 0.6757 (p-90) REVERT: C 421 TYR cc_start: 0.8060 (m-10) cc_final: 0.7803 (m-10) REVERT: C 516 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6564 (pp20) REVERT: C 532 ASN cc_start: 0.8947 (m-40) cc_final: 0.8701 (t0) REVERT: C 740 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7962 (ttt) outliers start: 36 outliers final: 19 residues processed: 185 average time/residue: 0.4906 time to fit residues: 107.0583 Evaluate side-chains 172 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 260 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 205 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 762 GLN A 779 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086730 restraints weight = 33379.266| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.45 r_work: 0.3026 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22427 Z= 0.229 Angle : 0.599 10.593 30637 Z= 0.300 Chirality : 0.048 0.316 3647 Planarity : 0.004 0.050 3861 Dihedral : 5.024 54.119 4052 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.48 % Allowed : 11.20 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2651 helix: 2.33 (0.20), residues: 641 sheet: 0.13 (0.20), residues: 617 loop : -0.56 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.022 0.002 TYR C1067 PHE 0.022 0.002 PHE A 898 TRP 0.028 0.002 TRP C 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00530 (22337) covalent geometry : angle 0.57177 (30401) SS BOND : bond 0.00234 ( 34) SS BOND : angle 1.23162 ( 68) hydrogen bonds : bond 0.04719 ( 953) hydrogen bonds : angle 5.63277 ( 2793) link_BETA1-4 : bond 0.00302 ( 18) link_BETA1-4 : angle 1.17583 ( 54) link_NAG-ASN : bond 0.00679 ( 38) link_NAG-ASN : angle 2.79259 ( 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 176 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 200 TYR cc_start: 0.7561 (m-80) cc_final: 0.6608 (t80) REVERT: A 221 SER cc_start: 0.8690 (t) cc_final: 0.8268 (p) REVERT: A 231 ILE cc_start: 0.8723 (pt) cc_final: 0.8475 (pp) REVERT: A 569 ILE cc_start: 0.8586 (mp) cc_final: 0.8129 (tp) REVERT: A 591 SER cc_start: 0.8803 (m) cc_final: 0.8375 (p) REVERT: A 821 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 858 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8778 (mt) REVERT: A 868 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: B 565 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7112 (p90) REVERT: B 983 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7597 (mtm-85) REVERT: C 52 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8642 (tm-30) REVERT: C 129 LYS cc_start: 0.6589 (mtmt) cc_final: 0.6103 (mmtt) REVERT: C 190 ARG cc_start: 0.7284 (mtt180) cc_final: 0.7011 (mmm160) REVERT: C 238 PHE cc_start: 0.5938 (p90) cc_final: 0.4707 (p90) REVERT: C 269 TYR cc_start: 0.7142 (m-80) cc_final: 0.6787 (m-80) REVERT: C 353 TRP cc_start: 0.7081 (p-90) cc_final: 0.6862 (p-90) REVERT: C 421 TYR cc_start: 0.7947 (m-10) cc_final: 0.7736 (m-10) REVERT: C 516 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6366 (pp20) REVERT: C 532 ASN cc_start: 0.8921 (m-40) cc_final: 0.8621 (t0) REVERT: C 740 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8044 (ttt) outliers start: 35 outliers final: 19 residues processed: 167 average time/residue: 0.4333 time to fit residues: 86.3945 Evaluate side-chains 163 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 217 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 170 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 762 GLN B1002 GLN C 955 ASN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.150834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088517 restraints weight = 33286.429| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.46 r_work: 0.3055 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22427 Z= 0.129 Angle : 0.564 16.186 30637 Z= 0.279 Chirality : 0.047 0.694 3647 Planarity : 0.004 0.049 3861 Dihedral : 4.913 53.810 4052 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.27 % Allowed : 11.28 % Favored : 87.45 % 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: 0.59 (0.16), residues: 2651 helix: 2.54 (0.21), residues: 628 sheet: 0.20 (0.21), residues: 576 loop : -0.48 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.024 0.001 TYR B 170 PHE 0.024 0.001 PHE A 168 TRP 0.036 0.001 TRP C 104 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00283 (22337) covalent geometry : angle 0.53015 (30401) SS BOND : bond 0.00135 ( 34) SS BOND : angle 1.02863 ( 68) hydrogen bonds : bond 0.04164 ( 953) hydrogen bonds : angle 5.46849 ( 2793) link_BETA1-4 : bond 0.00310 ( 18) link_BETA1-4 : angle 1.05200 ( 54) link_NAG-ASN : bond 0.00656 ( 38) link_NAG-ASN : angle 3.08433 ( 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 174 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 200 TYR cc_start: 0.7607 (m-80) cc_final: 0.6665 (t80) REVERT: A 221 SER cc_start: 0.8672 (t) cc_final: 0.8288 (p) REVERT: A 231 ILE cc_start: 0.8715 (pt) cc_final: 0.8468 (pp) REVERT: A 569 ILE cc_start: 0.8584 (mp) cc_final: 0.8134 (tp) REVERT: A 591 SER cc_start: 0.8810 (m) cc_final: 0.8405 (p) REVERT: A 821 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 858 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8789 (mt) REVERT: A 868 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: B 565 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 983 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7589 (mtm-85) REVERT: C 52 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 129 LYS cc_start: 0.6586 (mtmt) cc_final: 0.6078 (mmtt) REVERT: C 238 PHE cc_start: 0.5903 (p90) cc_final: 0.4690 (p90) REVERT: C 269 TYR cc_start: 0.7149 (m-80) cc_final: 0.6801 (m-80) REVERT: C 421 TYR cc_start: 0.8057 (m-10) cc_final: 0.7786 (m-10) REVERT: C 516 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6398 (pp20) REVERT: C 532 ASN cc_start: 0.8929 (m-40) cc_final: 0.8627 (t0) REVERT: C 740 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7995 (ttt) outliers start: 30 outliers final: 18 residues processed: 166 average time/residue: 0.4900 time to fit residues: 95.9298 Evaluate side-chains 161 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 762 GLN A 779 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.149780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087432 restraints weight = 33342.320| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.44 r_work: 0.3035 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22427 Z= 0.183 Angle : 0.581 10.899 30637 Z= 0.290 Chirality : 0.047 0.512 3647 Planarity : 0.004 0.049 3861 Dihedral : 5.006 54.020 4052 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.18 % Allowed : 11.49 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2651 helix: 2.42 (0.21), residues: 638 sheet: 0.21 (0.21), residues: 575 loop : -0.55 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.021 0.001 TYR C1067 PHE 0.022 0.001 PHE B 238 TRP 0.030 0.002 TRP C 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00419 (22337) covalent geometry : angle 0.55264 (30401) SS BOND : bond 0.00174 ( 34) SS BOND : angle 1.00698 ( 68) hydrogen bonds : bond 0.04480 ( 953) hydrogen bonds : angle 5.56193 ( 2793) link_BETA1-4 : bond 0.00328 ( 18) link_BETA1-4 : angle 1.14451 ( 54) link_NAG-ASN : bond 0.00650 ( 38) link_NAG-ASN : angle 2.86368 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14235.12 seconds wall clock time: 241 minutes 9.01 seconds (14469.01 seconds total)