Starting phenix.real_space_refine on Thu Mar 5 11:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9j_25759/03_2026/7t9j_25759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9j_25759/03_2026/7t9j_25759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9j_25759/03_2026/7t9j_25759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9j_25759/03_2026/7t9j_25759.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9j_25759/03_2026/7t9j_25759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9j_25759/03_2026/7t9j_25759.cif" } resolution = 2.79 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= 0.015 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 95 5.16 5 C 13995 2.51 5 N 3573 2.21 5 O 4297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 21960 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6519 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 45, 'TRANS': 789} Chain breaks: 9 Chain: "B" Number of atoms: 6528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6528 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 9 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.35, per 1000 atoms: 0.24 Number of scatterers: 21960 At special positions: 0 Unit cell: (134, 143, 172, 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 95 16.00 O 4297 8.00 N 3573 7.00 C 13995 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.02 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=2.02 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 331 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " 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: 1.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5082 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 39 sheets defined 26.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.063A 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: 3.553A 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: 3.918A 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 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 1032 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.540A 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: 4.041A 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: 3.526A 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: 3.961A 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 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: 4.081A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.585A 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: 3.951A 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 386 through 389 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.599A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.856A 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: 3.521A 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: 3.969A 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 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: 4.126A 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 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.801A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.962A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.769A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.604A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.711A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A 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: 6.222A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A 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: 6.222A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.716A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.194A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.788A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.172A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.760A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.548A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.812A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.608A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.476A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.476A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.098A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.051A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.918A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.470A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.169A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.972A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.972A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.869A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.477A 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=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.450A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.450A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.322A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 1002 hydrogen bonds defined for protein. 2808 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: 6.67 Time building geometry restraints manager: 2.42 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: 6756 1.34 - 1.46: 5578 1.46 - 1.59: 9979 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 22435 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.93e+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 6.92e+00 ... (remaining 22430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 29763 2.44 - 4.87: 689 4.87 - 7.31: 49 7.31 - 9.75: 8 9.75 - 12.19: 1 Bond angle restraints: 30510 Sorted by residual: angle pdb=" N ALA C 372 " pdb=" CA ALA C 372 " pdb=" C ALA C 372 " ideal model delta sigma weight residual 109.81 122.00 -12.19 2.21e+00 2.05e-01 3.04e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 104.51 7.49 1.40e+00 5.10e-01 2.86e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.17 -5.47 1.22e+00 6.72e-01 2.01e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" CB ARG A 995 " pdb=" CG ARG A 995 " pdb=" CD ARG A 995 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 ... (remaining 30505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13048 17.81 - 35.62: 875 35.62 - 53.43: 167 53.43 - 71.24: 59 71.24 - 89.05: 27 Dihedral angle restraints: 14176 sinusoidal: 6312 harmonic: 7864 Sorted by residual: dihedral pdb=" CA CYS A 590 " pdb=" C CYS A 590 " pdb=" N SER A 591 " pdb=" CA SER A 591 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 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 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP B 578 " pdb=" CB ASP B 578 " pdb=" CG ASP B 578 " pdb=" OD1 ASP B 578 " ideal model delta sinusoidal sigma weight residual -30.00 -88.47 58.47 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 14173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2944 0.073 - 0.147: 659 0.147 - 0.220: 50 0.220 - 0.294: 3 0.294 - 0.367: 3 Chirality restraints: 3659 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 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+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 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+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 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3656 not shown) Planarity restraints: 3897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.059 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO C 373 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 954 " 0.018 2.00e-02 2.50e+03 2.52e-02 9.51e+00 pdb=" CG HIS A 954 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS A 954 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS A 954 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 954 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 954 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 954 " -0.016 2.00e-02 2.50e+03 2.30e-02 7.91e+00 pdb=" CG HIS B 954 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS B 954 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS B 954 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS B 954 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 954 " 0.001 2.00e-02 2.50e+03 ... (remaining 3894 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2919 2.76 - 3.29: 19848 3.29 - 3.83: 37805 3.83 - 4.36: 44066 4.36 - 4.90: 76249 Nonbonded interactions: 180887 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.279 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.300 3.040 ... (remaining 180882 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' and (resid 14 through 528 or resid 530 through 1307)) } 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: 5.420 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.140 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 : 0.006 0.082 22527 Z= 0.271 Angle : 0.888 15.123 30752 Z= 0.476 Chirality : 0.059 0.367 3659 Planarity : 0.007 0.085 3857 Dihedral : 13.015 89.053 8992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.22 % Rotamer: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % 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: 0.20 (0.15), residues: 2645 helix: 1.29 (0.18), residues: 618 sheet: 0.93 (0.20), residues: 596 loop : -0.74 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 995 TYR 0.032 0.003 TYR A1067 PHE 0.044 0.003 PHE B 981 TRP 0.040 0.003 TRP C 886 HIS 0.033 0.003 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00582 (22435) covalent geometry : angle 0.86046 (30510) SS BOND : bond 0.00333 ( 34) SS BOND : angle 1.22888 ( 68) hydrogen bonds : bond 0.11224 ( 951) hydrogen bonds : angle 7.42272 ( 2808) link_BETA1-4 : bond 0.00586 ( 18) link_BETA1-4 : angle 1.49959 ( 54) link_NAG-ASN : bond 0.00744 ( 40) link_NAG-ASN : angle 3.47558 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 441 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6949 (m90) cc_final: 0.6748 (m-70) REVERT: A 83 VAL cc_start: 0.7014 (t) cc_final: 0.6776 (p) REVERT: A 223 LEU cc_start: 0.6521 (mp) cc_final: 0.6096 (mp) REVERT: A 589 PRO cc_start: 0.5576 (Cg_exo) cc_final: 0.5232 (Cg_endo) REVERT: B 656 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7089 (m) REVERT: B 731 MET cc_start: 0.7406 (mtm) cc_final: 0.7181 (mtm) REVERT: B 859 THR cc_start: 0.6875 (p) cc_final: 0.6670 (m) REVERT: B 984 LEU cc_start: 0.8583 (mt) cc_final: 0.8378 (tp) REVERT: B 988 GLU cc_start: 0.7539 (mp0) cc_final: 0.7272 (mp0) REVERT: C 85 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8846 (Cg_endo) REVERT: C 271 GLN cc_start: 0.8162 (mp10) cc_final: 0.7865 (mp10) REVERT: C 353 TRP cc_start: 0.8248 (p-90) cc_final: 0.7594 (p-90) outliers start: 4 outliers final: 2 residues processed: 445 average time/residue: 0.4752 time to fit residues: 249.1018 Evaluate side-chains 207 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PRO Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 907 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN B 954 HIS B1005 GLN C 314 GLN C 580 GLN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.133889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083937 restraints weight = 44816.190| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.93 r_work: 0.3097 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22527 Z= 0.182 Angle : 0.692 13.696 30752 Z= 0.346 Chirality : 0.047 0.254 3659 Planarity : 0.005 0.062 3857 Dihedral : 6.612 59.725 4095 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.07 % Allowed : 10.81 % Favored : 86.12 % 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: 0.29 (0.15), residues: 2645 helix: 1.62 (0.20), residues: 636 sheet: 0.63 (0.21), residues: 536 loop : -0.61 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 44 TYR 0.023 0.002 TYR B1067 PHE 0.028 0.002 PHE C 220 TRP 0.023 0.002 TRP C 886 HIS 0.007 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00403 (22435) covalent geometry : angle 0.66075 (30510) SS BOND : bond 0.00309 ( 34) SS BOND : angle 1.80011 ( 68) hydrogen bonds : bond 0.04261 ( 951) hydrogen bonds : angle 5.97661 ( 2808) link_BETA1-4 : bond 0.00359 ( 18) link_BETA1-4 : angle 1.22252 ( 54) link_NAG-ASN : bond 0.00698 ( 40) link_NAG-ASN : angle 3.00654 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 248 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6934 (m90) cc_final: 0.6719 (m-70) REVERT: A 83 VAL cc_start: 0.7726 (t) cc_final: 0.7517 (p) REVERT: A 135 PHE cc_start: 0.7015 (m-80) cc_final: 0.6806 (m-80) REVERT: A 589 PRO cc_start: 0.5699 (Cg_exo) cc_final: 0.5484 (Cg_endo) REVERT: A 697 MET cc_start: 0.7749 (ptt) cc_final: 0.7385 (ptt) REVERT: A 756 TYR cc_start: 0.7819 (m-80) cc_final: 0.7551 (m-80) REVERT: A 900 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8725 (ttm) REVERT: A 985 ASP cc_start: 0.7344 (t0) cc_final: 0.7043 (p0) REVERT: B 133 PHE cc_start: 0.7873 (m-80) cc_final: 0.7518 (m-80) REVERT: B 276 LEU cc_start: 0.8174 (tp) cc_final: 0.7752 (tm) REVERT: B 309 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8401 (mp0) REVERT: B 740 MET cc_start: 0.8435 (tpt) cc_final: 0.8107 (tpp) REVERT: B 761 THR cc_start: 0.8574 (m) cc_final: 0.8330 (p) REVERT: B 764 LYS cc_start: 0.7949 (mttt) cc_final: 0.7736 (mtpm) REVERT: B 859 THR cc_start: 0.7062 (p) cc_final: 0.6847 (p) REVERT: B 907 ASN cc_start: 0.8438 (m110) cc_final: 0.8179 (m-40) REVERT: B 984 LEU cc_start: 0.8099 (mt) cc_final: 0.7733 (tp) REVERT: B 988 GLU cc_start: 0.8034 (mp0) cc_final: 0.7601 (mp0) REVERT: B 1050 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8803 (pmm) REVERT: C 200 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5808 (t80) REVERT: C 271 GLN cc_start: 0.8503 (mp10) cc_final: 0.8203 (mp10) REVERT: C 353 TRP cc_start: 0.8158 (p-90) cc_final: 0.7395 (p-90) REVERT: C 421 TYR cc_start: 0.8099 (m-10) cc_final: 0.7895 (m-10) REVERT: C 434 ILE cc_start: 0.5252 (OUTLIER) cc_final: 0.4981 (pt) REVERT: C 516 GLU cc_start: 0.7686 (pp20) cc_final: 0.7306 (pp20) REVERT: C 773 GLU cc_start: 0.8319 (tt0) cc_final: 0.7921 (tt0) REVERT: C 780 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8388 (mm-30) REVERT: C 957 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 983 ARG cc_start: 0.7191 (ttm-80) cc_final: 0.6628 (tpm170) REVERT: C 1142 GLN cc_start: 0.8633 (tp40) cc_final: 0.7848 (tm-30) outliers start: 73 outliers final: 15 residues processed: 293 average time/residue: 0.4439 time to fit residues: 156.2233 Evaluate side-chains 198 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 872 GLN A 955 ASN A1054 GLN B 125 ASN B 804 GLN C 121 ASN C 314 GLN C 450 ASN C 824 ASN C 965 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.133474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.083433 restraints weight = 45402.699| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.96 r_work: 0.3095 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22527 Z= 0.208 Angle : 0.675 14.723 30752 Z= 0.339 Chirality : 0.048 0.285 3659 Planarity : 0.005 0.052 3857 Dihedral : 5.854 58.988 4089 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.20 % Allowed : 12.03 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2645 helix: 1.64 (0.20), residues: 633 sheet: 0.50 (0.20), residues: 581 loop : -0.66 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 328 TYR 0.021 0.002 TYR A1067 PHE 0.074 0.002 PHE A 592 TRP 0.024 0.002 TRP C 104 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00466 (22435) covalent geometry : angle 0.64961 (30510) SS BOND : bond 0.00519 ( 34) SS BOND : angle 1.48367 ( 68) hydrogen bonds : bond 0.04476 ( 951) hydrogen bonds : angle 5.90871 ( 2808) link_BETA1-4 : bond 0.00363 ( 18) link_BETA1-4 : angle 1.35164 ( 54) link_NAG-ASN : bond 0.00829 ( 40) link_NAG-ASN : angle 2.71292 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8083 (tm-30) REVERT: A 83 VAL cc_start: 0.8072 (t) cc_final: 0.7512 (p) REVERT: A 97 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5003 (mmmm) REVERT: A 135 PHE cc_start: 0.6689 (m-80) cc_final: 0.6463 (m-80) REVERT: A 269 TYR cc_start: 0.7610 (m-80) cc_final: 0.6932 (m-80) REVERT: A 314 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8300 (tp-100) REVERT: A 964 LYS cc_start: 0.8850 (tppp) cc_final: 0.8645 (mttt) REVERT: A 979 ASP cc_start: 0.7952 (t0) cc_final: 0.7644 (t0) REVERT: A 985 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 55 PHE cc_start: 0.6860 (m-80) cc_final: 0.6363 (m-80) REVERT: B 238 PHE cc_start: 0.6626 (p90) cc_final: 0.6145 (p90) REVERT: B 240 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7888 (t) REVERT: B 313 TYR cc_start: 0.8393 (m-80) cc_final: 0.8115 (m-80) REVERT: B 314 GLN cc_start: 0.8701 (tt0) cc_final: 0.8312 (tm-30) REVERT: B 317 ASN cc_start: 0.8321 (m110) cc_final: 0.8089 (m110) REVERT: B 745 ASP cc_start: 0.6729 (p0) cc_final: 0.6506 (p0) REVERT: B 759 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: B 764 LYS cc_start: 0.8391 (mttt) cc_final: 0.8129 (mtpm) REVERT: C 200 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5978 (t80) REVERT: C 271 GLN cc_start: 0.8722 (mp10) cc_final: 0.8466 (mp10) REVERT: C 302 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8745 (p) REVERT: C 353 TRP cc_start: 0.8039 (p-90) cc_final: 0.7775 (p-90) REVERT: C 773 GLU cc_start: 0.8592 (tt0) cc_final: 0.8200 (tt0) REVERT: C 934 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6839 (mp) REVERT: C 947 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8548 (mttp) REVERT: C 954 HIS cc_start: 0.8669 (m90) cc_final: 0.8381 (m-70) REVERT: C 957 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 983 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.6742 (tpm170) REVERT: C 1050 MET cc_start: 0.9324 (ptm) cc_final: 0.8972 (ptm) REVERT: C 1142 GLN cc_start: 0.8745 (tp40) cc_final: 0.7959 (tm-30) outliers start: 76 outliers final: 18 residues processed: 267 average time/residue: 0.4508 time to fit residues: 144.2935 Evaluate side-chains 203 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 261 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A1005 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.133745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083230 restraints weight = 45332.517| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.00 r_work: 0.3084 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22527 Z= 0.149 Angle : 0.601 11.624 30752 Z= 0.299 Chirality : 0.045 0.264 3659 Planarity : 0.004 0.049 3857 Dihedral : 5.523 53.239 4089 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.40 % Allowed : 13.84 % Favored : 83.77 % 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: 0.34 (0.16), residues: 2645 helix: 1.83 (0.21), residues: 627 sheet: 0.33 (0.20), residues: 598 loop : -0.54 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 78 TYR 0.025 0.001 TYR C 741 PHE 0.023 0.001 PHE B 201 TRP 0.027 0.002 TRP C 104 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00339 (22435) covalent geometry : angle 0.57789 (30510) SS BOND : bond 0.00212 ( 34) SS BOND : angle 1.28339 ( 68) hydrogen bonds : bond 0.03889 ( 951) hydrogen bonds : angle 5.62986 ( 2808) link_BETA1-4 : bond 0.00300 ( 18) link_BETA1-4 : angle 1.08805 ( 54) link_NAG-ASN : bond 0.00547 ( 40) link_NAG-ASN : angle 2.49495 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 83 VAL cc_start: 0.7883 (t) cc_final: 0.7624 (p) REVERT: A 97 LYS cc_start: 0.5378 (OUTLIER) cc_final: 0.5035 (mmmm) REVERT: A 200 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: A 239 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7305 (mt0) REVERT: A 269 TYR cc_start: 0.7686 (m-80) cc_final: 0.6936 (m-80) REVERT: A 314 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8403 (tp-100) REVERT: A 773 GLU cc_start: 0.8631 (tt0) cc_final: 0.8388 (tt0) REVERT: A 950 ASP cc_start: 0.8502 (t0) cc_final: 0.8081 (t0) REVERT: A 964 LYS cc_start: 0.8909 (tppp) cc_final: 0.8663 (mttt) REVERT: A 979 ASP cc_start: 0.7892 (t0) cc_final: 0.7599 (t0) REVERT: B 55 PHE cc_start: 0.6757 (m-80) cc_final: 0.6390 (m-80) REVERT: B 140 PHE cc_start: 0.7530 (p90) cc_final: 0.7148 (p90) REVERT: B 238 PHE cc_start: 0.6689 (p90) cc_final: 0.6307 (p90) REVERT: B 314 GLN cc_start: 0.8696 (tt0) cc_final: 0.8258 (tm-30) REVERT: B 759 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: B 764 LYS cc_start: 0.8419 (mttt) cc_final: 0.8179 (mtpm) REVERT: C 100 ILE cc_start: 0.8529 (mm) cc_final: 0.8266 (mm) REVERT: C 200 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6115 (t80) REVERT: C 242 LEU cc_start: 0.7398 (mt) cc_final: 0.7093 (mt) REVERT: C 271 GLN cc_start: 0.8776 (mp10) cc_final: 0.8543 (mp10) REVERT: C 353 TRP cc_start: 0.8137 (p-90) cc_final: 0.7885 (p-90) REVERT: C 749 CYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6748 (t) REVERT: C 773 GLU cc_start: 0.8680 (tt0) cc_final: 0.8293 (tt0) REVERT: C 859 THR cc_start: 0.9033 (m) cc_final: 0.8686 (p) REVERT: C 934 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6783 (mp) REVERT: C 947 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8506 (mttt) REVERT: C 957 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 983 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.6862 (tpm170) REVERT: C 1050 MET cc_start: 0.9279 (ptm) cc_final: 0.8920 (ptm) REVERT: C 1142 GLN cc_start: 0.8747 (tp40) cc_final: 0.8000 (tm-30) outliers start: 57 outliers final: 21 residues processed: 232 average time/residue: 0.4519 time to fit residues: 125.4605 Evaluate side-chains 196 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 231 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B1011 GLN C 450 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.132366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081384 restraints weight = 45250.570| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.99 r_work: 0.3041 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22527 Z= 0.189 Angle : 0.615 10.086 30752 Z= 0.306 Chirality : 0.046 0.277 3659 Planarity : 0.004 0.045 3857 Dihedral : 5.219 52.423 4089 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.69 % Allowed : 13.92 % Favored : 83.39 % 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: 0.31 (0.16), residues: 2645 helix: 1.87 (0.20), residues: 640 sheet: 0.21 (0.20), residues: 615 loop : -0.56 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 TYR 0.021 0.002 TYR B1067 PHE 0.022 0.002 PHE A 133 TRP 0.043 0.002 TRP C 104 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00434 (22435) covalent geometry : angle 0.59163 (30510) SS BOND : bond 0.00414 ( 34) SS BOND : angle 1.38142 ( 68) hydrogen bonds : bond 0.04000 ( 951) hydrogen bonds : angle 5.66713 ( 2808) link_BETA1-4 : bond 0.00277 ( 18) link_BETA1-4 : angle 1.13800 ( 54) link_NAG-ASN : bond 0.00568 ( 40) link_NAG-ASN : angle 2.49321 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 200 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.5734 (m-80) REVERT: A 269 TYR cc_start: 0.7831 (m-80) cc_final: 0.7010 (m-80) REVERT: A 314 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8387 (tp-100) REVERT: A 560 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 773 GLU cc_start: 0.8648 (tt0) cc_final: 0.8414 (tt0) REVERT: A 979 ASP cc_start: 0.8010 (t0) cc_final: 0.7700 (t0) REVERT: A 981 PHE cc_start: 0.7483 (m-80) cc_final: 0.7273 (m-10) REVERT: A 985 ASP cc_start: 0.7702 (p0) cc_final: 0.7424 (p0) REVERT: A 988 GLU cc_start: 0.8590 (mp0) cc_final: 0.8197 (mp0) REVERT: B 55 PHE cc_start: 0.7019 (m-80) cc_final: 0.6531 (m-80) REVERT: B 226 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6954 (tp) REVERT: B 238 PHE cc_start: 0.6831 (p90) cc_final: 0.6380 (p90) REVERT: B 240 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7973 (t) REVERT: B 314 GLN cc_start: 0.8670 (tt0) cc_final: 0.8203 (tm-30) REVERT: B 759 PHE cc_start: 0.8456 (m-80) cc_final: 0.8153 (m-80) REVERT: B 934 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 984 LEU cc_start: 0.8256 (mm) cc_final: 0.7541 (tp) REVERT: C 100 ILE cc_start: 0.8687 (mm) cc_final: 0.8460 (mm) REVERT: C 134 GLN cc_start: 0.9044 (tp40) cc_final: 0.8562 (mm110) REVERT: C 135 PHE cc_start: 0.7749 (m-80) cc_final: 0.7513 (m-80) REVERT: C 200 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6337 (t80) REVERT: C 242 LEU cc_start: 0.7479 (mt) cc_final: 0.7192 (mt) REVERT: C 302 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8896 (p) REVERT: C 324 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: C 353 TRP cc_start: 0.8192 (p-90) cc_final: 0.7769 (p-90) REVERT: C 421 TYR cc_start: 0.8158 (m-10) cc_final: 0.7954 (m-10) REVERT: C 586 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: C 661 GLU cc_start: 0.8223 (pp20) cc_final: 0.7917 (pp20) REVERT: C 749 CYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6532 (t) REVERT: C 859 THR cc_start: 0.9081 (m) cc_final: 0.8763 (p) REVERT: C 983 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.6901 (tpm170) REVERT: C 1050 MET cc_start: 0.9291 (ptm) cc_final: 0.9001 (ptm) REVERT: C 1142 GLN cc_start: 0.8748 (tp40) cc_final: 0.8088 (tm-30) outliers start: 64 outliers final: 22 residues processed: 235 average time/residue: 0.4665 time to fit residues: 130.2109 Evaluate side-chains 200 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 194 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 258 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 66 HIS B 125 ASN B 317 ASN C 121 ASN C 388 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082449 restraints weight = 44905.342| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.95 r_work: 0.3065 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22527 Z= 0.136 Angle : 0.581 10.941 30752 Z= 0.286 Chirality : 0.045 0.272 3659 Planarity : 0.004 0.061 3857 Dihedral : 4.971 53.222 4089 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.35 % Allowed : 14.55 % Favored : 83.10 % 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: 0.41 (0.16), residues: 2645 helix: 2.01 (0.21), residues: 641 sheet: 0.14 (0.20), residues: 581 loop : -0.45 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE C 592 TRP 0.028 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00308 (22435) covalent geometry : angle 0.56050 (30510) SS BOND : bond 0.00179 ( 34) SS BOND : angle 1.08126 ( 68) hydrogen bonds : bond 0.03696 ( 951) hydrogen bonds : angle 5.55876 ( 2808) link_BETA1-4 : bond 0.00337 ( 18) link_BETA1-4 : angle 0.97886 ( 54) link_NAG-ASN : bond 0.00521 ( 40) link_NAG-ASN : angle 2.36667 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 133 PHE cc_start: 0.7283 (m-80) cc_final: 0.7057 (m-80) REVERT: A 200 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: A 269 TYR cc_start: 0.7882 (m-80) cc_final: 0.7083 (m-80) REVERT: A 314 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8353 (tp-100) REVERT: A 560 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 773 GLU cc_start: 0.8662 (tt0) cc_final: 0.8389 (tt0) REVERT: A 964 LYS cc_start: 0.8936 (tppp) cc_final: 0.8686 (mtmm) REVERT: A 979 ASP cc_start: 0.8025 (t0) cc_final: 0.7719 (t0) REVERT: A 981 PHE cc_start: 0.7600 (m-80) cc_final: 0.7080 (m-10) REVERT: A 985 ASP cc_start: 0.7771 (p0) cc_final: 0.7224 (p0) REVERT: A 988 GLU cc_start: 0.8686 (mp0) cc_final: 0.8255 (pm20) REVERT: A 1092 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: B 55 PHE cc_start: 0.7050 (m-80) cc_final: 0.6710 (m-80) REVERT: B 238 PHE cc_start: 0.6887 (p90) cc_final: 0.6437 (p90) REVERT: B 314 GLN cc_start: 0.8539 (tt0) cc_final: 0.8136 (tm-30) REVERT: B 759 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: B 984 LEU cc_start: 0.8283 (mm) cc_final: 0.7560 (tp) REVERT: C 100 ILE cc_start: 0.8627 (mm) cc_final: 0.8392 (mm) REVERT: C 200 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6316 (t80) REVERT: C 242 LEU cc_start: 0.7450 (mt) cc_final: 0.7236 (mt) REVERT: C 302 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8922 (p) REVERT: C 324 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: C 353 TRP cc_start: 0.8165 (p-90) cc_final: 0.7709 (p-90) REVERT: C 661 GLU cc_start: 0.8201 (pp20) cc_final: 0.7862 (pp20) REVERT: C 749 CYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6287 (t) REVERT: C 859 THR cc_start: 0.9077 (m) cc_final: 0.8846 (p) REVERT: C 957 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 981 PHE cc_start: 0.8214 (m-10) cc_final: 0.8003 (m-10) REVERT: C 983 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.6910 (tpm170) REVERT: C 1050 MET cc_start: 0.9226 (ptm) cc_final: 0.8946 (ptm) REVERT: C 1142 GLN cc_start: 0.8772 (tp40) cc_final: 0.8112 (tm-30) outliers start: 56 outliers final: 26 residues processed: 219 average time/residue: 0.4580 time to fit residues: 119.5760 Evaluate side-chains 201 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 106 optimal weight: 6.9990 chunk 221 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 125 ASN A 137 ASN A 762 GLN A 872 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 115 GLN B 957 GLN B1005 GLN C 580 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.130307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.079134 restraints weight = 44971.970| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.95 r_work: 0.2996 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 22527 Z= 0.265 Angle : 0.654 10.230 30752 Z= 0.325 Chirality : 0.047 0.272 3659 Planarity : 0.004 0.048 3857 Dihedral : 5.122 51.826 4089 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.90 % Allowed : 14.21 % Favored : 82.88 % 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: 0.30 (0.16), residues: 2645 helix: 1.79 (0.20), residues: 638 sheet: 0.16 (0.20), residues: 621 loop : -0.50 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.028 0.002 TYR C 741 PHE 0.022 0.002 PHE C 592 TRP 0.026 0.002 TRP A 258 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00617 (22435) covalent geometry : angle 0.62822 (30510) SS BOND : bond 0.00393 ( 34) SS BOND : angle 2.07530 ( 68) hydrogen bonds : bond 0.04139 ( 951) hydrogen bonds : angle 5.78565 ( 2808) link_BETA1-4 : bond 0.00262 ( 18) link_BETA1-4 : angle 1.13383 ( 54) link_NAG-ASN : bond 0.00570 ( 40) link_NAG-ASN : angle 2.47676 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8414 (tm-30) REVERT: A 200 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5766 (m-80) REVERT: A 201 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 314 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8349 (tp-100) REVERT: A 560 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 755 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8514 (mp10) REVERT: A 773 GLU cc_start: 0.8748 (tt0) cc_final: 0.8513 (tt0) REVERT: A 919 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8502 (p0) REVERT: A 964 LYS cc_start: 0.8974 (tppp) cc_final: 0.8770 (mtmm) REVERT: A 979 ASP cc_start: 0.8037 (t0) cc_final: 0.7715 (t0) REVERT: A 985 ASP cc_start: 0.7853 (p0) cc_final: 0.7604 (p0) REVERT: A 988 GLU cc_start: 0.8685 (mp0) cc_final: 0.8280 (mp0) REVERT: B 237 ARG cc_start: 0.8790 (mtp180) cc_final: 0.8448 (mtm110) REVERT: B 238 PHE cc_start: 0.6790 (p90) cc_final: 0.6452 (p90) REVERT: B 314 GLN cc_start: 0.8569 (tt0) cc_final: 0.8128 (tm-30) REVERT: B 745 ASP cc_start: 0.6631 (p0) cc_final: 0.6428 (p0) REVERT: B 755 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7592 (mp10) REVERT: B 759 PHE cc_start: 0.8435 (m-80) cc_final: 0.8197 (m-80) REVERT: B 990 GLU cc_start: 0.8432 (tt0) cc_final: 0.8150 (tm-30) REVERT: B 1002 GLN cc_start: 0.8743 (pp30) cc_final: 0.8450 (pp30) REVERT: C 54 LEU cc_start: 0.8563 (pp) cc_final: 0.8308 (tt) REVERT: C 134 GLN cc_start: 0.9098 (tp40) cc_final: 0.8552 (mm110) REVERT: C 200 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6679 (t80) REVERT: C 302 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 353 TRP cc_start: 0.8142 (p-90) cc_final: 0.7643 (p-90) REVERT: C 749 CYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6509 (t) REVERT: C 859 THR cc_start: 0.9078 (m) cc_final: 0.8709 (p) REVERT: C 983 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.6936 (tpm170) REVERT: C 990 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 1050 MET cc_start: 0.9333 (ptm) cc_final: 0.9012 (ptm) REVERT: C 1142 GLN cc_start: 0.8821 (tp40) cc_final: 0.8158 (tm-30) outliers start: 69 outliers final: 34 residues processed: 224 average time/residue: 0.4568 time to fit residues: 121.9543 Evaluate side-chains 196 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 155 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 83 optimal weight: 40.0000 chunk 169 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 87 ASN A 125 ASN A 137 ASN A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.130895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080316 restraints weight = 44596.973| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.93 r_work: 0.3007 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22527 Z= 0.172 Angle : 0.618 10.849 30752 Z= 0.307 Chirality : 0.046 0.273 3659 Planarity : 0.004 0.052 3857 Dihedral : 5.002 52.940 4089 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.98 % Allowed : 15.39 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2645 helix: 1.83 (0.20), residues: 647 sheet: 0.12 (0.20), residues: 616 loop : -0.45 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.021 0.001 TYR C 265 PHE 0.028 0.001 PHE C 981 TRP 0.032 0.002 TRP C 104 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00395 (22435) covalent geometry : angle 0.59585 (30510) SS BOND : bond 0.00217 ( 34) SS BOND : angle 1.67957 ( 68) hydrogen bonds : bond 0.03842 ( 951) hydrogen bonds : angle 5.69789 ( 2808) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 0.98427 ( 54) link_NAG-ASN : bond 0.00501 ( 40) link_NAG-ASN : angle 2.33543 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 102 ARG cc_start: 0.6868 (mmp80) cc_final: 0.6430 (tpp80) REVERT: A 133 PHE cc_start: 0.7348 (m-80) cc_final: 0.7141 (m-10) REVERT: A 200 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.5808 (m-80) REVERT: A 201 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6491 (t80) REVERT: A 314 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8325 (tp-100) REVERT: A 773 GLU cc_start: 0.8722 (tt0) cc_final: 0.8268 (tt0) REVERT: A 919 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8482 (p0) REVERT: A 964 LYS cc_start: 0.8998 (tppp) cc_final: 0.8780 (mtmm) REVERT: A 979 ASP cc_start: 0.8051 (t0) cc_final: 0.7717 (t0) REVERT: A 985 ASP cc_start: 0.7881 (p0) cc_final: 0.7575 (p0) REVERT: A 988 GLU cc_start: 0.8665 (mp0) cc_final: 0.8251 (mp0) REVERT: B 55 PHE cc_start: 0.7429 (m-80) cc_final: 0.6936 (m-80) REVERT: B 238 PHE cc_start: 0.6838 (p90) cc_final: 0.6451 (p90) REVERT: B 314 GLN cc_start: 0.8498 (tt0) cc_final: 0.8105 (tm-30) REVERT: B 752 LEU cc_start: 0.8858 (tp) cc_final: 0.8048 (tp) REVERT: B 755 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7585 (mp10) REVERT: B 759 PHE cc_start: 0.8366 (m-80) cc_final: 0.8125 (m-80) REVERT: B 1002 GLN cc_start: 0.8724 (pp30) cc_final: 0.8427 (pp30) REVERT: C 134 GLN cc_start: 0.9128 (tp40) cc_final: 0.8501 (mm110) REVERT: C 135 PHE cc_start: 0.7449 (m-80) cc_final: 0.7207 (m-80) REVERT: C 200 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6807 (t80) REVERT: C 302 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 324 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: C 353 TRP cc_start: 0.8119 (p-90) cc_final: 0.7619 (p-90) REVERT: C 749 CYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6326 (t) REVERT: C 859 THR cc_start: 0.9074 (m) cc_final: 0.8809 (p) REVERT: C 957 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 983 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7045 (tpm170) REVERT: C 990 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 1050 MET cc_start: 0.9306 (ptm) cc_final: 0.8921 (ptm) REVERT: C 1142 GLN cc_start: 0.8840 (tp40) cc_final: 0.8189 (tm-30) outliers start: 47 outliers final: 28 residues processed: 197 average time/residue: 0.4640 time to fit residues: 109.2344 Evaluate side-chains 189 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 125 ASN A 762 GLN B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.127938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076978 restraints weight = 44758.880| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.92 r_work: 0.2941 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 22527 Z= 0.345 Angle : 0.738 13.514 30752 Z= 0.369 Chirality : 0.050 0.275 3659 Planarity : 0.005 0.058 3857 Dihedral : 5.476 50.244 4089 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.10 % Allowed : 15.48 % Favored : 82.42 % 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: -0.02 (0.16), residues: 2645 helix: 1.49 (0.20), residues: 637 sheet: -0.02 (0.20), residues: 582 loop : -0.69 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.023 0.002 TYR A1067 PHE 0.032 0.002 PHE C 342 TRP 0.034 0.002 TRP C 104 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00800 (22435) covalent geometry : angle 0.71264 (30510) SS BOND : bond 0.00398 ( 34) SS BOND : angle 2.29439 ( 68) hydrogen bonds : bond 0.04576 ( 951) hydrogen bonds : angle 6.07900 ( 2808) link_BETA1-4 : bond 0.00277 ( 18) link_BETA1-4 : angle 1.22199 ( 54) link_NAG-ASN : bond 0.00667 ( 40) link_NAG-ASN : angle 2.59994 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 133 PHE cc_start: 0.7522 (m-80) cc_final: 0.7240 (m-80) REVERT: A 200 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.5773 (m-80) REVERT: A 201 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6683 (t80) REVERT: A 314 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8293 (tp-100) REVERT: A 564 GLN cc_start: 0.7069 (mp10) cc_final: 0.6619 (mm110) REVERT: A 919 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (p0) REVERT: A 964 LYS cc_start: 0.8982 (tppp) cc_final: 0.8659 (mttt) REVERT: A 979 ASP cc_start: 0.8239 (t0) cc_final: 0.7894 (t0) REVERT: A 985 ASP cc_start: 0.7965 (p0) cc_final: 0.7630 (p0) REVERT: A 988 GLU cc_start: 0.8682 (mp0) cc_final: 0.8257 (mp0) REVERT: B 55 PHE cc_start: 0.7850 (m-80) cc_final: 0.7557 (m-80) REVERT: B 104 TRP cc_start: 0.7292 (m-90) cc_final: 0.6920 (m100) REVERT: B 238 PHE cc_start: 0.6861 (p90) cc_final: 0.6415 (p90) REVERT: B 314 GLN cc_start: 0.8447 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 547 LYS cc_start: 0.8307 (mttt) cc_final: 0.7960 (mtpp) REVERT: B 740 MET cc_start: 0.8539 (tpt) cc_final: 0.8259 (tpt) REVERT: B 752 LEU cc_start: 0.8932 (tp) cc_final: 0.8240 (tt) REVERT: B 755 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7685 (mp10) REVERT: B 759 PHE cc_start: 0.8401 (m-80) cc_final: 0.8162 (m-80) REVERT: C 134 GLN cc_start: 0.9136 (tp40) cc_final: 0.8522 (mm110) REVERT: C 200 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6899 (t80) REVERT: C 302 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9022 (p) REVERT: C 740 MET cc_start: 0.8734 (tpp) cc_final: 0.8486 (ttt) REVERT: C 759 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7526 (t80) REVERT: C 983 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7142 (tpm170) REVERT: C 990 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7350 (mt-10) REVERT: C 1050 MET cc_start: 0.9374 (ptm) cc_final: 0.9143 (ptm) REVERT: C 1142 GLN cc_start: 0.8822 (tp40) cc_final: 0.8245 (tm-30) outliers start: 50 outliers final: 30 residues processed: 197 average time/residue: 0.4885 time to fit residues: 113.4938 Evaluate side-chains 183 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 198 optimal weight: 0.0060 chunk 65 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 138 optimal weight: 0.0020 chunk 186 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.6006 ------------------------------------------------------------------------------- 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 125 ASN A 762 GLN A 872 GLN B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.130456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.080050 restraints weight = 44691.981| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.95 r_work: 0.3024 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 22527 Z= 0.145 Angle : 0.650 14.146 30752 Z= 0.323 Chirality : 0.046 0.275 3659 Planarity : 0.004 0.058 3857 Dihedral : 5.125 54.845 4089 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.51 % Allowed : 16.53 % Favored : 81.96 % 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: 0.14 (0.16), residues: 2645 helix: 1.69 (0.20), residues: 635 sheet: -0.04 (0.20), residues: 589 loop : -0.56 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.029 0.001 TYR B 170 PHE 0.027 0.001 PHE C 135 TRP 0.046 0.002 TRP C 104 HIS 0.003 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00332 (22435) covalent geometry : angle 0.62596 (30510) SS BOND : bond 0.00273 ( 34) SS BOND : angle 2.30513 ( 68) hydrogen bonds : bond 0.03907 ( 951) hydrogen bonds : angle 5.83557 ( 2808) link_BETA1-4 : bond 0.00398 ( 18) link_BETA1-4 : angle 0.94919 ( 54) link_NAG-ASN : bond 0.00500 ( 40) link_NAG-ASN : angle 2.27488 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8473 (tm-30) REVERT: A 97 LYS cc_start: 0.5727 (OUTLIER) cc_final: 0.5197 (mmmm) REVERT: A 102 ARG cc_start: 0.6828 (mmp80) cc_final: 0.6381 (tpp80) REVERT: A 133 PHE cc_start: 0.7488 (m-80) cc_final: 0.7180 (m-80) REVERT: A 200 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: A 201 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 269 TYR cc_start: 0.7539 (m-10) cc_final: 0.7029 (m-80) REVERT: A 314 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8292 (tp-100) REVERT: A 564 GLN cc_start: 0.7014 (mp10) cc_final: 0.6639 (mm110) REVERT: A 592 PHE cc_start: 0.7279 (m-80) cc_final: 0.6806 (m-80) REVERT: A 773 GLU cc_start: 0.8648 (tt0) cc_final: 0.8197 (tt0) REVERT: A 964 LYS cc_start: 0.8992 (tppp) cc_final: 0.8671 (mttt) REVERT: A 979 ASP cc_start: 0.8217 (t0) cc_final: 0.7904 (t0) REVERT: A 985 ASP cc_start: 0.7807 (p0) cc_final: 0.7476 (p0) REVERT: A 988 GLU cc_start: 0.8621 (mp0) cc_final: 0.8204 (mp0) REVERT: B 55 PHE cc_start: 0.7767 (m-80) cc_final: 0.7300 (m-80) REVERT: B 104 TRP cc_start: 0.7268 (m-90) cc_final: 0.6825 (m100) REVERT: B 238 PHE cc_start: 0.6858 (p90) cc_final: 0.6498 (p90) REVERT: B 314 GLN cc_start: 0.8357 (tt0) cc_final: 0.7898 (tm-30) REVERT: B 752 LEU cc_start: 0.8947 (tp) cc_final: 0.8336 (tt) REVERT: B 755 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7668 (mp10) REVERT: C 134 GLN cc_start: 0.9113 (tp40) cc_final: 0.8486 (mm110) REVERT: C 200 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6834 (t80) REVERT: C 302 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 353 TRP cc_start: 0.8446 (p-90) cc_final: 0.8229 (p-90) REVERT: C 859 THR cc_start: 0.9096 (m) cc_final: 0.8828 (p) REVERT: C 955 ASN cc_start: 0.8712 (t0) cc_final: 0.8448 (m-40) REVERT: C 983 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7109 (tpm170) REVERT: C 990 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7331 (mt-10) REVERT: C 1050 MET cc_start: 0.9238 (ptm) cc_final: 0.8926 (ptm) REVERT: C 1142 GLN cc_start: 0.8828 (tp40) cc_final: 0.8251 (tm-30) outliers start: 36 outliers final: 25 residues processed: 190 average time/residue: 0.4993 time to fit residues: 111.9018 Evaluate side-chains 180 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 55 optimal weight: 0.0370 chunk 169 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 88 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 166 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.131088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080815 restraints weight = 44765.039| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.95 r_work: 0.3043 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.7517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22527 Z= 0.127 Angle : 0.623 12.198 30752 Z= 0.308 Chirality : 0.046 0.280 3659 Planarity : 0.004 0.055 3857 Dihedral : 4.898 53.688 4089 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 1.39 % Allowed : 16.90 % Favored : 81.71 % 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: 0.26 (0.16), residues: 2645 helix: 1.80 (0.20), residues: 641 sheet: 0.01 (0.20), residues: 592 loop : -0.48 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.021 0.001 TYR C 265 PHE 0.021 0.001 PHE A 92 TRP 0.045 0.002 TRP C 353 HIS 0.004 0.000 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00286 (22435) covalent geometry : angle 0.60333 (30510) SS BOND : bond 0.00522 ( 34) SS BOND : angle 1.67640 ( 68) hydrogen bonds : bond 0.03751 ( 951) hydrogen bonds : angle 5.73909 ( 2808) link_BETA1-4 : bond 0.00365 ( 18) link_BETA1-4 : angle 0.96637 ( 54) link_NAG-ASN : bond 0.00485 ( 40) link_NAG-ASN : angle 2.20470 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9488.04 seconds wall clock time: 161 minutes 42.28 seconds (9702.28 seconds total)