Starting phenix.real_space_refine on Thu Jun 19 04:08:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf3_25860/06_2025/7tf3_25860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf3_25860/06_2025/7tf3_25860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf3_25860/06_2025/7tf3_25860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf3_25860/06_2025/7tf3_25860.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf3_25860/06_2025/7tf3_25860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf3_25860/06_2025/7tf3_25860.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 13909 2.51 5 N 3583 2.21 5 O 4289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21873 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6500 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6500 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8089 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.42, per 1000 atoms: 0.61 Number of scatterers: 21873 At special positions: 0 Unit cell: (141, 147, 174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 4289 8.00 N 3583 7.00 C 13909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 2.6 seconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 45 sheets defined 26.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.055A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.925A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.562A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.975A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.592A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.531A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.513A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.992A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.664A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.556A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.914A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.662A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.946A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.521A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.205A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.553A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.835A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.964A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.730A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 144 removed outlier: 7.063A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.678A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.705A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.661A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.340A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.109A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.712A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.707A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.237A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.563A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.596A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.107A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.109A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.024A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.556A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.831A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.838A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.887A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.683A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.239A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.290A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.64 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6619 1.34 - 1.46: 5557 1.46 - 1.58: 10054 1.58 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22346 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 22341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 29186 1.92 - 3.84: 1110 3.84 - 5.75: 89 5.75 - 7.67: 26 7.67 - 9.59: 8 Bond angle restraints: 30419 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.44 -5.74 1.22e+00 6.72e-01 2.22e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.37 -5.67 1.22e+00 6.72e-01 2.16e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.00 -5.30 1.22e+00 6.72e-01 1.89e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.36 -4.43 1.20e+00 6.94e-01 1.36e+01 ... (remaining 30414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12964 17.93 - 35.86: 870 35.86 - 53.79: 150 53.79 - 71.73: 55 71.73 - 89.66: 25 Dihedral angle restraints: 14064 sinusoidal: 6209 harmonic: 7855 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -57.50 -28.50 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 14061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2712 0.059 - 0.117: 774 0.117 - 0.175: 140 0.175 - 0.234: 23 0.234 - 0.292: 5 Chirality restraints: 3654 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3651 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.50e-02 5.61e+00 pdb=" CG TRP A 886 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C MET C 902 " 0.041 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.41e+00 pdb=" CG TRP C 886 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.003 2.00e-02 2.50e+03 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5876 2.81 - 3.33: 18476 3.33 - 3.85: 37465 3.85 - 4.38: 43155 4.38 - 4.90: 73914 Nonbonded interactions: 178886 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.329 3.040 ... (remaining 178881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 51.660 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22436 Z= 0.247 Angle : 0.858 14.917 30655 Z= 0.452 Chirality : 0.057 0.292 3654 Planarity : 0.006 0.055 3860 Dihedral : 12.938 89.657 8892 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2651 helix: 1.28 (0.19), residues: 607 sheet: 0.71 (0.20), residues: 582 loop : -0.74 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 886 HIS 0.004 0.001 HIS C1083 PHE 0.034 0.002 PHE A 275 TYR 0.035 0.003 TYR C1067 ARG 0.005 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 38) link_NAG-ASN : angle 3.82542 ( 114) link_BETA1-4 : bond 0.00802 ( 18) link_BETA1-4 : angle 1.60192 ( 54) hydrogen bonds : bond 0.12160 ( 958) hydrogen bonds : angle 7.34017 ( 2790) SS BOND : bond 0.00334 ( 34) SS BOND : angle 1.29406 ( 68) covalent geometry : bond 0.00521 (22346) covalent geometry : angle 0.82346 (30419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7716 (tp) cc_final: 0.7495 (mp) REVERT: A 205 SER cc_start: 0.8576 (t) cc_final: 0.8375 (m) REVERT: A 240 THR cc_start: 0.7857 (m) cc_final: 0.7220 (t) REVERT: A 697 MET cc_start: 0.8976 (ptt) cc_final: 0.8767 (ptt) REVERT: A 994 ASP cc_start: 0.8067 (t70) cc_final: 0.7837 (t0) REVERT: B 190 ARG cc_start: 0.7063 (mpt-90) cc_final: 0.6478 (mmm160) REVERT: B 206 LYS cc_start: 0.7724 (tppt) cc_final: 0.7424 (tmtt) REVERT: B 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8033 (pt) REVERT: B 987 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8087 (Cg_endo) REVERT: B 1029 MET cc_start: 0.9123 (tpp) cc_final: 0.8555 (tpp) REVERT: C 269 TYR cc_start: 0.7308 (m-80) cc_final: 0.7005 (m-80) REVERT: C 351 TYR cc_start: 0.7831 (p90) cc_final: 0.7465 (p90) REVERT: C 378 LYS cc_start: 0.8273 (ttmt) cc_final: 0.8022 (ttpp) REVERT: C 408 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7249 (ptm160) REVERT: C 453 TYR cc_start: 0.5453 (p90) cc_final: 0.5151 (p90) REVERT: C 586 ASP cc_start: 0.7260 (t70) cc_final: 0.6987 (t0) REVERT: C 858 LEU cc_start: 0.8638 (mp) cc_final: 0.8169 (tp) REVERT: C 1029 MET cc_start: 0.9296 (tpp) cc_final: 0.9078 (tpp) outliers start: 0 outliers final: 2 residues processed: 288 average time/residue: 1.3889 time to fit residues: 454.9775 Evaluate side-chains 137 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain C residue 574 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 755 GLN A 926 GLN A 954 GLN A1002 GLN A1071 HIS B 764 ASN B 824 ASN B 901 GLN B 955 ASN B 960 ASN B1011 GLN C 580 GLN C 606 ASN C 954 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080093 restraints weight = 37556.029| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.58 r_work: 0.3038 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22436 Z= 0.272 Angle : 0.667 10.541 30655 Z= 0.338 Chirality : 0.049 0.247 3654 Planarity : 0.005 0.046 3860 Dihedral : 7.107 107.336 4056 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.98 % Allowed : 7.13 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 2651 helix: 1.99 (0.21), residues: 622 sheet: 0.54 (0.20), residues: 648 loop : -0.61 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 886 HIS 0.006 0.001 HIS C 207 PHE 0.025 0.002 PHE A 275 TYR 0.028 0.002 TYR C 28 ARG 0.011 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 38) link_NAG-ASN : angle 3.12425 ( 114) link_BETA1-4 : bond 0.00216 ( 18) link_BETA1-4 : angle 1.26992 ( 54) hydrogen bonds : bond 0.05149 ( 958) hydrogen bonds : angle 6.05841 ( 2790) SS BOND : bond 0.00312 ( 34) SS BOND : angle 1.10614 ( 68) covalent geometry : bond 0.00628 (22346) covalent geometry : angle 0.63698 (30419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7672 (tp) cc_final: 0.7303 (mp) REVERT: A 200 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 240 THR cc_start: 0.8050 (m) cc_final: 0.7755 (t) REVERT: A 994 ASP cc_start: 0.8737 (t70) cc_final: 0.8530 (t0) REVERT: A 1010 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7833 (mp-120) REVERT: B 571 ASP cc_start: 0.8377 (m-30) cc_final: 0.7950 (t70) REVERT: B 580 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: B 858 LEU cc_start: 0.9003 (mt) cc_final: 0.8196 (pt) REVERT: B 987 PRO cc_start: 0.8172 (Cg_exo) cc_final: 0.7833 (Cg_endo) REVERT: C 200 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6574 (t80) REVERT: C 269 TYR cc_start: 0.7573 (m-80) cc_final: 0.6782 (m-80) REVERT: C 309 GLU cc_start: 0.7779 (mp0) cc_final: 0.7214 (pm20) REVERT: C 378 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7764 (ttpp) REVERT: C 408 ARG cc_start: 0.7634 (ptt90) cc_final: 0.7081 (ptp90) REVERT: C 436 TRP cc_start: 0.6301 (OUTLIER) cc_final: 0.4840 (p-90) REVERT: C 740 MET cc_start: 0.9144 (tpp) cc_final: 0.8767 (ttt) REVERT: C 780 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8825 (mm-30) REVERT: C 964 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (mtmt) REVERT: C 987 PRO cc_start: 0.8701 (Cg_exo) cc_final: 0.8328 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7797 (mp0) outliers start: 47 outliers final: 16 residues processed: 174 average time/residue: 1.1232 time to fit residues: 229.7640 Evaluate side-chains 136 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 263 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 251 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 955 ASN B 960 ASN B1002 GLN C 52 GLN C 99 ASN C 121 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.135071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082086 restraints weight = 37255.335| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.52 r_work: 0.3071 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22436 Z= 0.136 Angle : 0.573 11.139 30655 Z= 0.285 Chirality : 0.045 0.263 3654 Planarity : 0.004 0.040 3860 Dihedral : 6.383 58.319 4052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.86 % Allowed : 8.40 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2651 helix: 2.40 (0.21), residues: 623 sheet: 0.53 (0.20), residues: 638 loop : -0.51 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.002 0.001 HIS C 207 PHE 0.021 0.001 PHE C 377 TYR 0.023 0.001 TYR C 28 ARG 0.005 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 38) link_NAG-ASN : angle 3.17894 ( 114) link_BETA1-4 : bond 0.00367 ( 18) link_BETA1-4 : angle 1.02557 ( 54) hydrogen bonds : bond 0.04310 ( 958) hydrogen bonds : angle 5.72127 ( 2790) SS BOND : bond 0.00132 ( 34) SS BOND : angle 0.73683 ( 68) covalent geometry : bond 0.00301 (22346) covalent geometry : angle 0.53831 (30419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6018 (t80) REVERT: A 240 THR cc_start: 0.8112 (m) cc_final: 0.7842 (t) REVERT: A 964 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8542 (mppt) REVERT: A 994 ASP cc_start: 0.8738 (t70) cc_final: 0.8529 (t0) REVERT: B 269 TYR cc_start: 0.7437 (m-80) cc_final: 0.7021 (m-80) REVERT: B 571 ASP cc_start: 0.8348 (m-30) cc_final: 0.7936 (t70) REVERT: B 580 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6815 (mt0) REVERT: B 858 LEU cc_start: 0.9062 (mt) cc_final: 0.8199 (pt) REVERT: B 987 PRO cc_start: 0.8102 (Cg_exo) cc_final: 0.7840 (Cg_endo) REVERT: C 52 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7932 (tp-100) REVERT: C 135 PHE cc_start: 0.7157 (t80) cc_final: 0.6885 (t80) REVERT: C 200 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6539 (t80) REVERT: C 269 TYR cc_start: 0.7481 (m-80) cc_final: 0.6780 (m-80) REVERT: C 309 GLU cc_start: 0.7850 (mp0) cc_final: 0.7220 (pm20) REVERT: C 316 SER cc_start: 0.8770 (t) cc_final: 0.8556 (p) REVERT: C 378 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7723 (ttpp) REVERT: C 408 ARG cc_start: 0.7657 (ptt90) cc_final: 0.7127 (ptp90) REVERT: C 436 TRP cc_start: 0.6283 (OUTLIER) cc_final: 0.4906 (p-90) REVERT: C 505 TYR cc_start: 0.7139 (p90) cc_final: 0.6927 (p90) REVERT: C 646 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8090 (ttp80) REVERT: C 740 MET cc_start: 0.9171 (tpp) cc_final: 0.8762 (ttt) REVERT: C 964 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8806 (mtmt) REVERT: C 987 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8311 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7827 (tm-30) outliers start: 44 outliers final: 14 residues processed: 158 average time/residue: 1.1710 time to fit residues: 216.4001 Evaluate side-chains 137 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 227 optimal weight: 0.0050 chunk 209 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN A 824 ASN B 960 ASN C 779 GLN C 824 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.132583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079226 restraints weight = 37598.306| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.57 r_work: 0.3016 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22436 Z= 0.259 Angle : 0.633 10.457 30655 Z= 0.317 Chirality : 0.048 0.273 3654 Planarity : 0.004 0.043 3860 Dihedral : 6.101 58.219 4052 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 9.29 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2651 helix: 2.36 (0.21), residues: 617 sheet: 0.23 (0.19), residues: 662 loop : -0.57 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.005 0.001 HIS C 207 PHE 0.020 0.002 PHE A 898 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 38) link_NAG-ASN : angle 3.29200 ( 114) link_BETA1-4 : bond 0.00223 ( 18) link_BETA1-4 : angle 1.23214 ( 54) hydrogen bonds : bond 0.04952 ( 958) hydrogen bonds : angle 5.82451 ( 2790) SS BOND : bond 0.00262 ( 34) SS BOND : angle 0.88186 ( 68) covalent geometry : bond 0.00600 (22346) covalent geometry : angle 0.59893 (30419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6236 (t80) REVERT: A 994 ASP cc_start: 0.8804 (t70) cc_final: 0.8447 (t70) REVERT: B 53 ASP cc_start: 0.7000 (t70) cc_final: 0.6717 (t70) REVERT: B 190 ARG cc_start: 0.6863 (mpt-90) cc_final: 0.6432 (mmm-85) REVERT: B 269 TYR cc_start: 0.7517 (m-80) cc_final: 0.7089 (m-80) REVERT: B 571 ASP cc_start: 0.8308 (m-30) cc_final: 0.8010 (t70) REVERT: B 580 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: B 592 PHE cc_start: 0.7902 (p90) cc_final: 0.7629 (p90) REVERT: B 987 PRO cc_start: 0.8072 (Cg_exo) cc_final: 0.7795 (Cg_endo) REVERT: B 1142 GLN cc_start: 0.8393 (tp40) cc_final: 0.8016 (tm-30) REVERT: C 135 PHE cc_start: 0.7067 (t80) cc_final: 0.6790 (t80) REVERT: C 200 TYR cc_start: 0.6813 (t80) cc_final: 0.6589 (t80) REVERT: C 316 SER cc_start: 0.8858 (t) cc_final: 0.8527 (p) REVERT: C 378 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7783 (ttpp) REVERT: C 436 TRP cc_start: 0.6415 (OUTLIER) cc_final: 0.4926 (p-90) REVERT: C 505 TYR cc_start: 0.7210 (p90) cc_final: 0.6978 (p90) REVERT: C 531 THR cc_start: 0.8620 (m) cc_final: 0.8067 (p) REVERT: C 619 GLU cc_start: 0.7583 (mp0) cc_final: 0.7321 (mp0) REVERT: C 646 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8055 (ttp80) REVERT: C 964 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8826 (mtmt) REVERT: C 987 PRO cc_start: 0.8585 (Cg_exo) cc_final: 0.8196 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7966 (tm-30) outliers start: 53 outliers final: 19 residues processed: 162 average time/residue: 1.1032 time to fit residues: 210.8748 Evaluate side-chains 139 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 156 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 137 optimal weight: 0.0980 chunk 139 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN B 580 GLN B 960 ASN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.133991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081207 restraints weight = 37322.919| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.52 r_work: 0.3057 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22436 Z= 0.122 Angle : 0.550 10.525 30655 Z= 0.275 Chirality : 0.044 0.265 3654 Planarity : 0.004 0.040 3860 Dihedral : 5.575 57.850 4052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.65 % Allowed : 10.43 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2651 helix: 2.63 (0.21), residues: 618 sheet: 0.34 (0.20), residues: 623 loop : -0.49 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS C 207 PHE 0.020 0.001 PHE B 238 TYR 0.024 0.001 TYR A 170 ARG 0.004 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 38) link_NAG-ASN : angle 3.01825 ( 114) link_BETA1-4 : bond 0.00404 ( 18) link_BETA1-4 : angle 1.01865 ( 54) hydrogen bonds : bond 0.04139 ( 958) hydrogen bonds : angle 5.52510 ( 2790) SS BOND : bond 0.00110 ( 34) SS BOND : angle 0.66392 ( 68) covalent geometry : bond 0.00267 (22346) covalent geometry : angle 0.51796 (30419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6223 (t80) REVERT: A 569 ILE cc_start: 0.8632 (mp) cc_final: 0.8422 (pt) REVERT: A 586 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: A 964 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8468 (mppt) REVERT: A 994 ASP cc_start: 0.8775 (t70) cc_final: 0.8524 (t0) REVERT: B 53 ASP cc_start: 0.7120 (t70) cc_final: 0.6839 (t70) REVERT: B 190 ARG cc_start: 0.6902 (mpt-90) cc_final: 0.6541 (mmm-85) REVERT: B 269 TYR cc_start: 0.7540 (m-80) cc_final: 0.7103 (m-80) REVERT: B 580 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6629 (mt0) REVERT: B 987 PRO cc_start: 0.8007 (Cg_exo) cc_final: 0.7754 (Cg_endo) REVERT: C 64 TRP cc_start: 0.6623 (t60) cc_final: 0.6158 (t-100) REVERT: C 135 PHE cc_start: 0.7066 (t80) cc_final: 0.6747 (t80) REVERT: C 278 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7744 (tttm) REVERT: C 309 GLU cc_start: 0.7850 (mp0) cc_final: 0.7314 (pm20) REVERT: C 316 SER cc_start: 0.8869 (t) cc_final: 0.8574 (p) REVERT: C 378 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7724 (ttpp) REVERT: C 436 TRP cc_start: 0.6338 (OUTLIER) cc_final: 0.4904 (p-90) REVERT: C 505 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7149 (p90) REVERT: C 531 THR cc_start: 0.8693 (m) cc_final: 0.8165 (p) REVERT: C 619 GLU cc_start: 0.7660 (mp0) cc_final: 0.7386 (mp0) REVERT: C 646 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8004 (ttp80) REVERT: C 740 MET cc_start: 0.9173 (tpp) cc_final: 0.8726 (ttt) REVERT: C 964 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8894 (mtmt) REVERT: C 987 PRO cc_start: 0.8539 (Cg_exo) cc_final: 0.8149 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7935 (tm-30) outliers start: 39 outliers final: 14 residues processed: 148 average time/residue: 1.1354 time to fit residues: 199.2550 Evaluate side-chains 137 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 190 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 125 ASN A 196 ASN A 239 GLN B1002 GLN C 52 GLN C 394 ASN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.132921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079699 restraints weight = 37263.076| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.53 r_work: 0.3031 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22436 Z= 0.191 Angle : 0.583 13.062 30655 Z= 0.291 Chirality : 0.046 0.265 3654 Planarity : 0.004 0.038 3860 Dihedral : 5.517 55.240 4052 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.73 % Allowed : 10.85 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2651 helix: 2.59 (0.21), residues: 624 sheet: 0.19 (0.20), residues: 646 loop : -0.53 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.003 0.001 HIS C 207 PHE 0.028 0.002 PHE A 238 TYR 0.023 0.002 TYR A 170 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 38) link_NAG-ASN : angle 3.24847 ( 114) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.08437 ( 54) hydrogen bonds : bond 0.04445 ( 958) hydrogen bonds : angle 5.56076 ( 2790) SS BOND : bond 0.00176 ( 34) SS BOND : angle 0.75534 ( 68) covalent geometry : bond 0.00440 (22346) covalent geometry : angle 0.54779 (30419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6218 (t80) REVERT: A 569 ILE cc_start: 0.8653 (mp) cc_final: 0.8435 (pt) REVERT: A 964 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8518 (tppt) REVERT: A 994 ASP cc_start: 0.8792 (t70) cc_final: 0.8541 (t0) REVERT: B 53 ASP cc_start: 0.7127 (t70) cc_final: 0.6789 (t70) REVERT: B 190 ARG cc_start: 0.6931 (mpt-90) cc_final: 0.6469 (mmm-85) REVERT: B 207 HIS cc_start: 0.7378 (t-170) cc_final: 0.7007 (t-90) REVERT: B 269 TYR cc_start: 0.7615 (m-80) cc_final: 0.7175 (m-80) REVERT: B 569 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8344 (pt) REVERT: B 580 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: B 987 PRO cc_start: 0.7961 (Cg_exo) cc_final: 0.7738 (Cg_endo) REVERT: B 1142 GLN cc_start: 0.8374 (tp40) cc_final: 0.8010 (tm-30) REVERT: C 64 TRP cc_start: 0.6570 (t60) cc_final: 0.6122 (t-100) REVERT: C 135 PHE cc_start: 0.7020 (t80) cc_final: 0.6761 (t80) REVERT: C 278 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7709 (tttm) REVERT: C 309 GLU cc_start: 0.7919 (mp0) cc_final: 0.7349 (pm20) REVERT: C 316 SER cc_start: 0.8871 (t) cc_final: 0.8566 (p) REVERT: C 378 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7725 (ttpp) REVERT: C 436 TRP cc_start: 0.6385 (OUTLIER) cc_final: 0.4901 (p-90) REVERT: C 505 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.7107 (p90) REVERT: C 531 THR cc_start: 0.8674 (m) cc_final: 0.8167 (p) REVERT: C 619 GLU cc_start: 0.7697 (mp0) cc_final: 0.7385 (mp0) REVERT: C 646 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: C 740 MET cc_start: 0.9182 (tpp) cc_final: 0.8782 (ttt) REVERT: C 820 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: C 964 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8777 (mtmt) REVERT: C 987 PRO cc_start: 0.8509 (Cg_exo) cc_final: 0.8121 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7943 (tm-30) outliers start: 41 outliers final: 17 residues processed: 152 average time/residue: 1.0971 time to fit residues: 197.3512 Evaluate side-chains 145 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 132 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.134005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080925 restraints weight = 37342.447| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.3060 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22436 Z= 0.120 Angle : 0.544 12.094 30655 Z= 0.272 Chirality : 0.044 0.263 3654 Planarity : 0.003 0.039 3860 Dihedral : 5.182 52.289 4052 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.65 % Allowed : 11.48 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2651 helix: 2.74 (0.21), residues: 624 sheet: 0.29 (0.20), residues: 621 loop : -0.46 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.000 HIS C 207 PHE 0.027 0.001 PHE B 201 TYR 0.024 0.001 TYR A 170 ARG 0.003 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 38) link_NAG-ASN : angle 3.04691 ( 114) link_BETA1-4 : bond 0.00360 ( 18) link_BETA1-4 : angle 0.98045 ( 54) hydrogen bonds : bond 0.03950 ( 958) hydrogen bonds : angle 5.35538 ( 2790) SS BOND : bond 0.00114 ( 34) SS BOND : angle 0.66350 ( 68) covalent geometry : bond 0.00266 (22346) covalent geometry : angle 0.51030 (30419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 2.242 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7705 (tp) cc_final: 0.7231 (mt) REVERT: A 200 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6188 (t80) REVERT: A 569 ILE cc_start: 0.8647 (mp) cc_final: 0.8418 (pt) REVERT: A 586 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: A 821 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 964 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8467 (mppt) REVERT: A 994 ASP cc_start: 0.8760 (t70) cc_final: 0.8501 (t0) REVERT: B 53 ASP cc_start: 0.7030 (t70) cc_final: 0.6752 (t70) REVERT: B 190 ARG cc_start: 0.6874 (mpt-90) cc_final: 0.6529 (mmm-85) REVERT: B 207 HIS cc_start: 0.7402 (t-170) cc_final: 0.7092 (t-90) REVERT: B 269 TYR cc_start: 0.7523 (m-80) cc_final: 0.7138 (m-80) REVERT: B 569 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8356 (pt) REVERT: C 135 PHE cc_start: 0.6912 (t80) cc_final: 0.6698 (t80) REVERT: C 200 TYR cc_start: 0.6671 (t80) cc_final: 0.6409 (t80) REVERT: C 278 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7900 (tttt) REVERT: C 309 GLU cc_start: 0.7897 (mp0) cc_final: 0.7341 (pm20) REVERT: C 316 SER cc_start: 0.8833 (t) cc_final: 0.8558 (p) REVERT: C 320 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7685 (m) REVERT: C 378 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7774 (ttpp) REVERT: C 436 TRP cc_start: 0.6327 (OUTLIER) cc_final: 0.5078 (p-90) REVERT: C 505 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.7084 (p90) REVERT: C 531 THR cc_start: 0.8726 (m) cc_final: 0.8213 (p) REVERT: C 586 ASP cc_start: 0.7131 (t70) cc_final: 0.6587 (t0) REVERT: C 619 GLU cc_start: 0.7785 (mp0) cc_final: 0.7375 (mp0) REVERT: C 646 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7961 (ttp80) REVERT: C 740 MET cc_start: 0.9160 (tpp) cc_final: 0.8729 (ttt) REVERT: C 964 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8719 (mtmt) REVERT: C 987 PRO cc_start: 0.8459 (Cg_exo) cc_final: 0.8075 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7926 (tm-30) outliers start: 39 outliers final: 18 residues processed: 153 average time/residue: 1.1972 time to fit residues: 217.0607 Evaluate side-chains 147 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 215 optimal weight: 2.9990 chunk 242 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 238 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 960 ASN C 52 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.134085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.081009 restraints weight = 37226.817| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.53 r_work: 0.3063 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22436 Z= 0.121 Angle : 0.539 12.348 30655 Z= 0.270 Chirality : 0.044 0.263 3654 Planarity : 0.003 0.039 3860 Dihedral : 4.955 52.244 4052 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.52 % Allowed : 11.95 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2651 helix: 2.76 (0.21), residues: 617 sheet: 0.36 (0.20), residues: 630 loop : -0.42 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 64 HIS 0.004 0.001 HIS C 66 PHE 0.018 0.001 PHE A 140 TYR 0.026 0.001 TYR A 170 ARG 0.003 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 38) link_NAG-ASN : angle 3.00485 ( 114) link_BETA1-4 : bond 0.00327 ( 18) link_BETA1-4 : angle 1.01849 ( 54) hydrogen bonds : bond 0.03938 ( 958) hydrogen bonds : angle 5.26815 ( 2790) SS BOND : bond 0.00110 ( 34) SS BOND : angle 0.65162 ( 68) covalent geometry : bond 0.00268 (22346) covalent geometry : angle 0.50650 (30419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7628 (tp) cc_final: 0.7200 (mt) REVERT: A 200 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 569 ILE cc_start: 0.8644 (mp) cc_final: 0.8438 (pt) REVERT: A 586 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: A 821 LEU cc_start: 0.8627 (tt) cc_final: 0.8215 (mp) REVERT: A 964 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8465 (mppt) REVERT: A 994 ASP cc_start: 0.8745 (t70) cc_final: 0.8480 (t0) REVERT: B 53 ASP cc_start: 0.6984 (t70) cc_final: 0.6713 (t70) REVERT: B 189 LEU cc_start: 0.7601 (mt) cc_final: 0.7327 (mt) REVERT: B 190 ARG cc_start: 0.6892 (mpt-90) cc_final: 0.6449 (mmm-85) REVERT: B 207 HIS cc_start: 0.7410 (t-170) cc_final: 0.7081 (t-90) REVERT: B 269 TYR cc_start: 0.7395 (m-80) cc_final: 0.7068 (m-80) REVERT: B 569 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8390 (pt) REVERT: C 64 TRP cc_start: 0.6775 (t60) cc_final: 0.6087 (t-100) REVERT: C 135 PHE cc_start: 0.6878 (t80) cc_final: 0.6662 (t80) REVERT: C 278 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7919 (tttt) REVERT: C 309 GLU cc_start: 0.7896 (mp0) cc_final: 0.7343 (pm20) REVERT: C 316 SER cc_start: 0.8835 (t) cc_final: 0.8571 (p) REVERT: C 342 PHE cc_start: 0.8367 (m-80) cc_final: 0.6713 (p90) REVERT: C 378 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7798 (ttpp) REVERT: C 436 TRP cc_start: 0.6253 (OUTLIER) cc_final: 0.5167 (p-90) REVERT: C 505 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.7075 (p90) REVERT: C 531 THR cc_start: 0.8700 (m) cc_final: 0.8181 (p) REVERT: C 586 ASP cc_start: 0.7118 (t70) cc_final: 0.6599 (t0) REVERT: C 619 GLU cc_start: 0.7803 (mp0) cc_final: 0.7417 (mp0) REVERT: C 646 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7964 (ttp80) REVERT: C 740 MET cc_start: 0.9152 (tpp) cc_final: 0.8698 (ttt) REVERT: C 820 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: C 964 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8699 (mtmt) REVERT: C 987 PRO cc_start: 0.8514 (Cg_exo) cc_final: 0.8156 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7942 (tm-30) outliers start: 36 outliers final: 17 residues processed: 147 average time/residue: 1.1264 time to fit residues: 195.5433 Evaluate side-chains 143 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 238 optimal weight: 0.4980 chunk 52 optimal weight: 0.0470 chunk 259 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.133505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080308 restraints weight = 37308.015| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.54 r_work: 0.3049 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22436 Z= 0.150 Angle : 0.554 12.349 30655 Z= 0.278 Chirality : 0.045 0.263 3654 Planarity : 0.004 0.039 3860 Dihedral : 4.952 51.696 4052 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 12.11 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2651 helix: 2.75 (0.21), residues: 617 sheet: 0.40 (0.20), residues: 637 loop : -0.45 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.002 0.001 HIS C 207 PHE 0.034 0.001 PHE A 238 TYR 0.025 0.001 TYR A 170 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 38) link_NAG-ASN : angle 3.03534 ( 114) link_BETA1-4 : bond 0.00305 ( 18) link_BETA1-4 : angle 1.02647 ( 54) hydrogen bonds : bond 0.04093 ( 958) hydrogen bonds : angle 5.32761 ( 2790) SS BOND : bond 0.00122 ( 34) SS BOND : angle 0.66630 ( 68) covalent geometry : bond 0.00342 (22346) covalent geometry : angle 0.52156 (30419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 5.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7637 (tp) cc_final: 0.7195 (mt) REVERT: A 200 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 569 ILE cc_start: 0.8644 (mp) cc_final: 0.8408 (pt) REVERT: A 586 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: A 821 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8235 (mp) REVERT: A 964 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8383 (mttt) REVERT: A 994 ASP cc_start: 0.8776 (t70) cc_final: 0.8513 (t0) REVERT: B 53 ASP cc_start: 0.6963 (t70) cc_final: 0.6710 (t70) REVERT: B 189 LEU cc_start: 0.7602 (mt) cc_final: 0.7257 (mt) REVERT: B 190 ARG cc_start: 0.6864 (mpt-90) cc_final: 0.6473 (mmm160) REVERT: B 269 TYR cc_start: 0.7405 (m-80) cc_final: 0.7072 (m-80) REVERT: B 1142 GLN cc_start: 0.8381 (tp40) cc_final: 0.8060 (tm-30) REVERT: C 53 ASP cc_start: 0.7102 (t70) cc_final: 0.6897 (t0) REVERT: C 64 TRP cc_start: 0.6781 (t60) cc_final: 0.6106 (t-100) REVERT: C 278 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7797 (tttt) REVERT: C 309 GLU cc_start: 0.7929 (mp0) cc_final: 0.7360 (pm20) REVERT: C 316 SER cc_start: 0.8849 (t) cc_final: 0.8581 (p) REVERT: C 342 PHE cc_start: 0.8360 (m-80) cc_final: 0.6716 (p90) REVERT: C 378 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7806 (ttpp) REVERT: C 421 TYR cc_start: 0.8134 (m-10) cc_final: 0.7507 (m-10) REVERT: C 436 TRP cc_start: 0.6200 (OUTLIER) cc_final: 0.5136 (p-90) REVERT: C 505 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.7080 (p90) REVERT: C 516 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: C 531 THR cc_start: 0.8719 (m) cc_final: 0.8210 (p) REVERT: C 586 ASP cc_start: 0.7062 (t70) cc_final: 0.6525 (t0) REVERT: C 619 GLU cc_start: 0.7822 (mp0) cc_final: 0.7422 (mp0) REVERT: C 646 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7979 (ttp80) REVERT: C 740 MET cc_start: 0.9151 (tpp) cc_final: 0.8710 (ttt) REVERT: C 820 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: C 964 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8717 (mtmt) REVERT: C 987 PRO cc_start: 0.8472 (Cg_exo) cc_final: 0.8094 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7940 (tm-30) outliers start: 38 outliers final: 18 residues processed: 152 average time/residue: 1.3634 time to fit residues: 245.5157 Evaluate side-chains 150 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 159 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 90 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 239 GLN B 580 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.133598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080365 restraints weight = 37568.979| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.55 r_work: 0.3052 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22436 Z= 0.142 Angle : 0.554 12.374 30655 Z= 0.277 Chirality : 0.045 0.264 3654 Planarity : 0.003 0.040 3860 Dihedral : 4.921 51.707 4052 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.44 % Allowed : 12.33 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2651 helix: 2.75 (0.21), residues: 617 sheet: 0.38 (0.20), residues: 645 loop : -0.43 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.002 0.001 HIS B1064 PHE 0.030 0.001 PHE B 201 TYR 0.026 0.001 TYR A 170 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 38) link_NAG-ASN : angle 3.03643 ( 114) link_BETA1-4 : bond 0.00327 ( 18) link_BETA1-4 : angle 1.02537 ( 54) hydrogen bonds : bond 0.04047 ( 958) hydrogen bonds : angle 5.30185 ( 2790) SS BOND : bond 0.00122 ( 34) SS BOND : angle 0.66368 ( 68) covalent geometry : bond 0.00322 (22346) covalent geometry : angle 0.52120 (30419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7653 (tp) cc_final: 0.7228 (mt) REVERT: A 129 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6641 (ttmt) REVERT: A 200 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6310 (t80) REVERT: A 569 ILE cc_start: 0.8646 (mp) cc_final: 0.8401 (pt) REVERT: A 586 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: A 821 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 994 ASP cc_start: 0.8765 (t70) cc_final: 0.8499 (t0) REVERT: B 53 ASP cc_start: 0.6971 (t70) cc_final: 0.6724 (t70) REVERT: B 269 TYR cc_start: 0.7428 (m-80) cc_final: 0.7095 (m-80) REVERT: C 53 ASP cc_start: 0.7087 (t70) cc_final: 0.6862 (t0) REVERT: C 64 TRP cc_start: 0.6802 (t60) cc_final: 0.6130 (t-100) REVERT: C 278 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7815 (tttt) REVERT: C 309 GLU cc_start: 0.7921 (mp0) cc_final: 0.7350 (pm20) REVERT: C 316 SER cc_start: 0.8850 (t) cc_final: 0.8594 (p) REVERT: C 342 PHE cc_start: 0.8368 (m-80) cc_final: 0.6717 (p90) REVERT: C 378 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7817 (ttpp) REVERT: C 421 TYR cc_start: 0.8184 (m-10) cc_final: 0.7562 (m-10) REVERT: C 436 TRP cc_start: 0.6205 (OUTLIER) cc_final: 0.5193 (p-90) REVERT: C 505 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.7078 (p90) REVERT: C 516 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: C 531 THR cc_start: 0.8726 (m) cc_final: 0.8225 (p) REVERT: C 586 ASP cc_start: 0.7071 (t70) cc_final: 0.6538 (t0) REVERT: C 619 GLU cc_start: 0.7828 (mp0) cc_final: 0.7412 (mp0) REVERT: C 646 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: C 740 MET cc_start: 0.9151 (tpp) cc_final: 0.8698 (ttt) REVERT: C 820 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: C 964 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8708 (mtmt) REVERT: C 987 PRO cc_start: 0.8472 (Cg_exo) cc_final: 0.8095 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7946 (tm-30) outliers start: 34 outliers final: 18 residues processed: 147 average time/residue: 1.1383 time to fit residues: 199.0035 Evaluate side-chains 149 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 224 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 254 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079260 restraints weight = 37270.476| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.54 r_work: 0.3025 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22436 Z= 0.191 Angle : 0.589 12.388 30655 Z= 0.295 Chirality : 0.046 0.263 3654 Planarity : 0.004 0.039 3860 Dihedral : 5.130 50.931 4052 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.44 % Allowed : 12.37 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2651 helix: 2.65 (0.21), residues: 617 sheet: 0.27 (0.20), residues: 644 loop : -0.50 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.003 0.001 HIS C 207 PHE 0.020 0.002 PHE A 79 TYR 0.025 0.002 TYR A 170 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 38) link_NAG-ASN : angle 3.17178 ( 114) link_BETA1-4 : bond 0.00269 ( 18) link_BETA1-4 : angle 1.09621 ( 54) hydrogen bonds : bond 0.04425 ( 958) hydrogen bonds : angle 5.47995 ( 2790) SS BOND : bond 0.00154 ( 34) SS BOND : angle 0.72102 ( 68) covalent geometry : bond 0.00441 (22346) covalent geometry : angle 0.55535 (30419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28198.81 seconds wall clock time: 487 minutes 33.30 seconds (29253.30 seconds total)