Starting phenix.real_space_refine on Thu Jun 19 05:17:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9j_25759/06_2025/7t9j_25759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9j_25759/06_2025/7t9j_25759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9j_25759/06_2025/7t9j_25759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9j_25759/06_2025/7t9j_25759.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9j_25759/06_2025/7t9j_25759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9j_25759/06_2025/7t9j_25759.cif" } resolution = 2.79 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 13995 2.51 5 N 3573 2.21 5 O 4297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21960 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6519 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 45, 'TRANS': 789} Chain breaks: 9 Chain: "B" Number of atoms: 6528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6528 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 9 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.76, per 1000 atoms: 0.63 Number of scatterers: 21960 At special positions: 0 Unit cell: (134, 143, 172, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 4297 8.00 N 3573 7.00 C 13995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5082 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 39 sheets defined 26.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.063A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.553A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.918A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.540A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.041A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.526A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.961A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.081A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.585A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.951A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.599A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.856A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.521A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.969A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.126A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.801A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.962A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.769A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.604A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.711A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.716A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.194A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.788A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.172A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.760A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.548A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.812A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.608A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.476A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.476A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.098A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.051A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.918A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.470A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.169A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.972A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.972A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.869A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.450A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.450A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.322A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 1002 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.36 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6756 1.34 - 1.46: 5578 1.46 - 1.59: 9979 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 22435 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 ... (remaining 22430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 29763 2.44 - 4.87: 689 4.87 - 7.31: 49 7.31 - 9.75: 8 9.75 - 12.19: 1 Bond angle restraints: 30510 Sorted by residual: angle pdb=" N ALA C 372 " pdb=" CA ALA C 372 " pdb=" C ALA C 372 " ideal model delta sigma weight residual 109.81 122.00 -12.19 2.21e+00 2.05e-01 3.04e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 104.51 7.49 1.40e+00 5.10e-01 2.86e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.17 -5.47 1.22e+00 6.72e-01 2.01e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" CB ARG A 995 " pdb=" CG ARG A 995 " pdb=" CD ARG A 995 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 ... (remaining 30505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13048 17.81 - 35.62: 875 35.62 - 53.43: 167 53.43 - 71.24: 59 71.24 - 89.05: 27 Dihedral angle restraints: 14176 sinusoidal: 6312 harmonic: 7864 Sorted by residual: dihedral pdb=" CA CYS A 590 " pdb=" C CYS A 590 " pdb=" N SER A 591 " pdb=" CA SER A 591 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP B 578 " pdb=" CB ASP B 578 " pdb=" CG ASP B 578 " pdb=" OD1 ASP B 578 " ideal model delta sinusoidal sigma weight residual -30.00 -88.47 58.47 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 14173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2944 0.073 - 0.147: 659 0.147 - 0.220: 50 0.220 - 0.294: 3 0.294 - 0.367: 3 Chirality restraints: 3659 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3656 not shown) Planarity restraints: 3897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.059 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO C 373 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 954 " 0.018 2.00e-02 2.50e+03 2.52e-02 9.51e+00 pdb=" CG HIS A 954 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS A 954 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS A 954 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 954 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 954 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 954 " -0.016 2.00e-02 2.50e+03 2.30e-02 7.91e+00 pdb=" CG HIS B 954 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS B 954 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS B 954 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS B 954 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 954 " 0.001 2.00e-02 2.50e+03 ... (remaining 3894 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2919 2.76 - 3.29: 19848 3.29 - 3.83: 37805 3.83 - 4.36: 44066 4.36 - 4.90: 76249 Nonbonded interactions: 180887 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.279 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.300 3.040 ... (remaining 180882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 528 or resid 530 through 1147 or resid 1301 thr \ ough 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 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: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 51.670 Find NCS groups from input model: 0.890 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 22527 Z= 0.271 Angle : 0.888 15.123 30752 Z= 0.476 Chirality : 0.059 0.367 3659 Planarity : 0.007 0.085 3857 Dihedral : 13.015 89.053 8992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.22 % Rotamer: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.15), residues: 2645 helix: 1.29 (0.18), residues: 618 sheet: 0.93 (0.20), residues: 596 loop : -0.74 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 886 HIS 0.033 0.003 HIS A 954 PHE 0.044 0.003 PHE B 981 TYR 0.032 0.003 TYR A1067 ARG 0.014 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 40) link_NAG-ASN : angle 3.47558 ( 120) link_BETA1-4 : bond 0.00586 ( 18) link_BETA1-4 : angle 1.49959 ( 54) hydrogen bonds : bond 0.11224 ( 951) hydrogen bonds : angle 7.42272 ( 2808) SS BOND : bond 0.00333 ( 34) SS BOND : angle 1.22888 ( 68) covalent geometry : bond 0.00582 (22435) covalent geometry : angle 0.86046 (30510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 441 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6949 (m90) cc_final: 0.6748 (m-70) REVERT: A 83 VAL cc_start: 0.7014 (t) cc_final: 0.6776 (p) REVERT: A 223 LEU cc_start: 0.6521 (mp) cc_final: 0.6096 (mp) REVERT: A 589 PRO cc_start: 0.5576 (Cg_exo) cc_final: 0.5232 (Cg_endo) REVERT: B 656 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7089 (m) REVERT: B 731 MET cc_start: 0.7406 (mtm) cc_final: 0.7181 (mtm) REVERT: B 859 THR cc_start: 0.6875 (p) cc_final: 0.6670 (m) REVERT: B 988 GLU cc_start: 0.7539 (mp0) cc_final: 0.7273 (mp0) REVERT: C 85 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8901 (Cg_endo) REVERT: C 271 GLN cc_start: 0.8162 (mp10) cc_final: 0.7865 (mp10) REVERT: C 353 TRP cc_start: 0.8248 (p-90) cc_final: 0.7595 (p-90) REVERT: C 913 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6342 (pt0) outliers start: 4 outliers final: 2 residues processed: 445 average time/residue: 0.9957 time to fit residues: 524.6232 Evaluate side-chains 208 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PRO Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 913 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 613 GLN A 907 ASN A 955 ASN A 965 GLN B 125 ASN B 901 GLN B 907 ASN B 954 HIS B1005 GLN C 314 GLN C 580 GLN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083857 restraints weight = 44600.773| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.93 r_work: 0.3125 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 22527 Z= 0.205 Angle : 0.714 11.038 30752 Z= 0.358 Chirality : 0.048 0.261 3659 Planarity : 0.005 0.061 3857 Dihedral : 6.712 59.989 4098 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.20 % Allowed : 10.56 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.15), residues: 2645 helix: 1.50 (0.20), residues: 637 sheet: 0.57 (0.21), residues: 555 loop : -0.62 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 886 HIS 0.009 0.001 HIS B 954 PHE 0.032 0.002 PHE C 220 TYR 0.025 0.002 TYR B 741 ARG 0.013 0.001 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.01280 ( 40) link_NAG-ASN : angle 2.92026 ( 120) link_BETA1-4 : bond 0.00479 ( 18) link_BETA1-4 : angle 1.35850 ( 54) hydrogen bonds : bond 0.04284 ( 951) hydrogen bonds : angle 5.98752 ( 2808) SS BOND : bond 0.00779 ( 34) SS BOND : angle 1.66256 ( 68) covalent geometry : bond 0.00457 (22435) covalent geometry : angle 0.68642 (30510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8121 (m-80) cc_final: 0.7912 (m-80) REVERT: A 92 PHE cc_start: 0.6253 (t80) cc_final: 0.5981 (t80) REVERT: A 97 LYS cc_start: 0.5482 (OUTLIER) cc_final: 0.4569 (mptp) REVERT: A 135 PHE cc_start: 0.7156 (m-80) cc_final: 0.6947 (m-80) REVERT: A 697 MET cc_start: 0.8033 (ptt) cc_final: 0.7806 (ptt) REVERT: A 900 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8882 (ttm) REVERT: A 985 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7108 (p0) REVERT: B 133 PHE cc_start: 0.7862 (m-80) cc_final: 0.7503 (m-80) REVERT: B 289 VAL cc_start: 0.7178 (t) cc_final: 0.6918 (t) REVERT: B 309 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8422 (mp0) REVERT: B 740 MET cc_start: 0.8466 (tpt) cc_final: 0.8178 (tpp) REVERT: B 761 THR cc_start: 0.8624 (m) cc_final: 0.8288 (p) REVERT: B 764 LYS cc_start: 0.8036 (mttt) cc_final: 0.7816 (mtpm) REVERT: B 859 THR cc_start: 0.7368 (p) cc_final: 0.7138 (p) REVERT: B 984 LEU cc_start: 0.8059 (tp) cc_final: 0.7768 (tp) REVERT: B 988 GLU cc_start: 0.8072 (mp0) cc_final: 0.7562 (mp0) REVERT: B 1050 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8916 (pmm) REVERT: C 134 GLN cc_start: 0.8868 (mm110) cc_final: 0.8544 (mm-40) REVERT: C 200 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5645 (t80) REVERT: C 271 GLN cc_start: 0.8574 (mp10) cc_final: 0.8301 (mp10) REVERT: C 338 PHE cc_start: 0.8607 (m-80) cc_final: 0.8211 (m-80) REVERT: C 353 TRP cc_start: 0.8179 (p-90) cc_final: 0.7397 (p-90) REVERT: C 434 ILE cc_start: 0.5551 (OUTLIER) cc_final: 0.5092 (pt) REVERT: C 516 GLU cc_start: 0.7712 (pp20) cc_final: 0.7271 (pp20) REVERT: C 773 GLU cc_start: 0.8439 (tt0) cc_final: 0.8108 (tt0) REVERT: C 933 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7241 (mttp) REVERT: C 957 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 983 ARG cc_start: 0.7135 (ttm-80) cc_final: 0.6657 (tpm170) REVERT: C 985 ASP cc_start: 0.7800 (p0) cc_final: 0.7317 (p0) REVERT: C 1142 GLN cc_start: 0.8718 (tp40) cc_final: 0.7888 (tm-30) outliers start: 76 outliers final: 16 residues processed: 300 average time/residue: 1.0488 time to fit residues: 375.2414 Evaluate side-chains 209 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 256 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 246 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 213 optimal weight: 9.9990 chunk 221 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1054 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 314 GLN C 450 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.134683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084796 restraints weight = 45275.270| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.98 r_work: 0.3134 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22527 Z= 0.140 Angle : 0.601 11.993 30752 Z= 0.300 Chirality : 0.045 0.279 3659 Planarity : 0.004 0.051 3857 Dihedral : 5.766 57.962 4089 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.69 % Allowed : 12.20 % Favored : 85.11 % 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: 0.43 (0.16), residues: 2645 helix: 1.91 (0.20), residues: 640 sheet: 0.52 (0.21), residues: 571 loop : -0.55 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.007 0.001 HIS A 954 PHE 0.043 0.002 PHE A 592 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 40) link_NAG-ASN : angle 2.59267 ( 120) link_BETA1-4 : bond 0.00466 ( 18) link_BETA1-4 : angle 1.09940 ( 54) hydrogen bonds : bond 0.03993 ( 951) hydrogen bonds : angle 5.71566 ( 2808) SS BOND : bond 0.00330 ( 34) SS BOND : angle 1.19519 ( 68) covalent geometry : bond 0.00310 (22435) covalent geometry : angle 0.57698 (30510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6453 (t80) cc_final: 0.6201 (t80) REVERT: A 97 LYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5206 (mmmm) REVERT: A 239 GLN cc_start: 0.6995 (mm110) cc_final: 0.6595 (mp10) REVERT: A 269 TYR cc_start: 0.7453 (m-80) cc_final: 0.6947 (m-80) REVERT: A 287 ASP cc_start: 0.7913 (t0) cc_final: 0.7658 (t0) REVERT: A 723 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 756 TYR cc_start: 0.8509 (m-80) cc_final: 0.8120 (m-80) REVERT: A 964 LYS cc_start: 0.8748 (tppp) cc_final: 0.8543 (mttt) REVERT: A 979 ASP cc_start: 0.7868 (t0) cc_final: 0.7593 (t0) REVERT: A 985 ASP cc_start: 0.7687 (t0) cc_final: 0.7432 (p0) REVERT: B 55 PHE cc_start: 0.6713 (m-80) cc_final: 0.6255 (m-80) REVERT: B 313 TYR cc_start: 0.8064 (m-80) cc_final: 0.7797 (m-80) REVERT: B 745 ASP cc_start: 0.6491 (p0) cc_final: 0.6201 (p0) REVERT: B 761 THR cc_start: 0.8665 (m) cc_final: 0.8454 (p) REVERT: B 764 LYS cc_start: 0.8223 (mttt) cc_final: 0.7778 (mtpm) REVERT: B 988 GLU cc_start: 0.8115 (mp0) cc_final: 0.7580 (mp0) REVERT: B 1002 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8081 (pp30) REVERT: B 1050 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8889 (ptm) REVERT: C 200 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5866 (t80) REVERT: C 271 GLN cc_start: 0.8626 (mp10) cc_final: 0.8360 (mp10) REVERT: C 302 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 353 TRP cc_start: 0.8019 (p-90) cc_final: 0.7817 (p-90) REVERT: C 421 TYR cc_start: 0.8153 (m-10) cc_final: 0.7926 (m-10) REVERT: C 773 GLU cc_start: 0.8535 (tt0) cc_final: 0.8202 (tt0) REVERT: C 933 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7231 (mtmm) REVERT: C 947 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8267 (mtpt) REVERT: C 954 HIS cc_start: 0.8598 (m90) cc_final: 0.8361 (m-70) REVERT: C 957 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 983 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.6858 (tpm170) REVERT: C 1142 GLN cc_start: 0.8735 (tp40) cc_final: 0.7948 (tm-30) outliers start: 64 outliers final: 16 residues processed: 247 average time/residue: 0.9737 time to fit residues: 290.3324 Evaluate side-chains 197 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 262 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 174 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN A 824 ASN B 125 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 314 GLN C 450 ASN C 580 GLN C 965 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.136367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085666 restraints weight = 45053.593| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.07 r_work: 0.3132 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 22527 Z= 0.127 Angle : 0.587 15.410 30752 Z= 0.290 Chirality : 0.045 0.268 3659 Planarity : 0.004 0.067 3857 Dihedral : 5.313 53.471 4089 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.73 % Allowed : 12.95 % Favored : 84.31 % 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: 0.45 (0.16), residues: 2645 helix: 1.86 (0.20), residues: 644 sheet: 0.43 (0.20), residues: 588 loop : -0.47 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 104 HIS 0.005 0.001 HIS A 954 PHE 0.018 0.001 PHE C 592 TYR 0.021 0.001 TYR C 741 ARG 0.012 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 40) link_NAG-ASN : angle 2.43620 ( 120) link_BETA1-4 : bond 0.00309 ( 18) link_BETA1-4 : angle 1.03769 ( 54) hydrogen bonds : bond 0.03751 ( 951) hydrogen bonds : angle 5.48539 ( 2808) SS BOND : bond 0.00153 ( 34) SS BOND : angle 1.38739 ( 68) covalent geometry : bond 0.00289 (22435) covalent geometry : angle 0.56355 (30510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6477 (t80) cc_final: 0.6205 (t80) REVERT: A 97 LYS cc_start: 0.5250 (OUTLIER) cc_final: 0.4932 (mmmm) REVERT: A 239 GLN cc_start: 0.6996 (mm110) cc_final: 0.6571 (mp10) REVERT: A 269 TYR cc_start: 0.7611 (m-80) cc_final: 0.7061 (m-80) REVERT: A 314 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8287 (tp-100) REVERT: A 756 TYR cc_start: 0.8489 (m-80) cc_final: 0.8139 (m-80) REVERT: A 979 ASP cc_start: 0.7851 (t0) cc_final: 0.7576 (t0) REVERT: B 238 PHE cc_start: 0.6929 (p90) cc_final: 0.6452 (p90) REVERT: B 240 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7885 (t) REVERT: B 314 GLN cc_start: 0.8646 (tt0) cc_final: 0.8240 (tm-30) REVERT: B 759 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 761 THR cc_start: 0.8771 (m) cc_final: 0.8510 (p) REVERT: B 764 LYS cc_start: 0.8262 (mttt) cc_final: 0.8020 (mtpm) REVERT: B 988 GLU cc_start: 0.8077 (mp0) cc_final: 0.7564 (mp0) REVERT: B 1002 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8057 (pp30) REVERT: B 1050 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8876 (ptm) REVERT: C 200 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5965 (t80) REVERT: C 242 LEU cc_start: 0.7474 (mt) cc_final: 0.7189 (mt) REVERT: C 271 GLN cc_start: 0.8667 (mp10) cc_final: 0.8350 (mp10) REVERT: C 353 TRP cc_start: 0.8141 (p-90) cc_final: 0.7900 (p-90) REVERT: C 749 CYS cc_start: 0.7239 (OUTLIER) cc_final: 0.7007 (t) REVERT: C 761 THR cc_start: 0.8243 (m) cc_final: 0.7905 (p) REVERT: C 773 GLU cc_start: 0.8566 (tt0) cc_final: 0.8219 (tt0) REVERT: C 859 THR cc_start: 0.9043 (m) cc_final: 0.8643 (p) REVERT: C 933 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7497 (mtmm) REVERT: C 947 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8309 (mtpt) REVERT: C 957 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 983 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.6881 (tpm170) REVERT: C 1142 GLN cc_start: 0.8724 (tp40) cc_final: 0.7951 (tm-30) outliers start: 65 outliers final: 21 residues processed: 239 average time/residue: 0.9330 time to fit residues: 268.9536 Evaluate side-chains 201 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 165 optimal weight: 0.0050 chunk 263 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN B 196 ASN B 804 GLN B 824 ASN B1011 GLN C 314 GLN C 450 ASN C 824 ASN C 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.131465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.080581 restraints weight = 45188.252| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.96 r_work: 0.3012 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 22527 Z= 0.255 Angle : 0.680 10.668 30752 Z= 0.341 Chirality : 0.048 0.280 3659 Planarity : 0.004 0.047 3857 Dihedral : 5.345 52.184 4089 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.86 % Allowed : 12.99 % Favored : 84.15 % 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: 0.22 (0.16), residues: 2645 helix: 1.63 (0.20), residues: 637 sheet: 0.23 (0.20), residues: 593 loop : -0.56 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 104 HIS 0.006 0.002 HIS B 66 PHE 0.022 0.002 PHE A 133 TYR 0.021 0.002 TYR B1067 ARG 0.007 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 40) link_NAG-ASN : angle 2.65623 ( 120) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.31652 ( 54) hydrogen bonds : bond 0.04479 ( 951) hydrogen bonds : angle 5.86273 ( 2808) SS BOND : bond 0.00323 ( 34) SS BOND : angle 1.83531 ( 68) covalent geometry : bond 0.00594 (22435) covalent geometry : angle 0.65435 (30510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7282 (t0) cc_final: 0.7012 (t0) REVERT: A 54 LEU cc_start: 0.8653 (mt) cc_final: 0.8398 (mm) REVERT: A 269 TYR cc_start: 0.7842 (m-80) cc_final: 0.7046 (m-80) REVERT: A 314 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8397 (tp-100) REVERT: A 773 GLU cc_start: 0.8750 (tt0) cc_final: 0.8405 (tt0) REVERT: A 964 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8704 (mttt) REVERT: A 979 ASP cc_start: 0.7951 (t0) cc_final: 0.7671 (t0) REVERT: A 985 ASP cc_start: 0.7697 (p0) cc_final: 0.7141 (p0) REVERT: A 988 GLU cc_start: 0.8693 (mp0) cc_final: 0.8284 (pm20) REVERT: B 226 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6983 (tp) REVERT: B 237 ARG cc_start: 0.8753 (mtp180) cc_final: 0.8423 (mtm110) REVERT: B 238 PHE cc_start: 0.6754 (p90) cc_final: 0.6429 (p90) REVERT: B 240 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (t) REVERT: B 310 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8933 (tmmm) REVERT: B 314 GLN cc_start: 0.8761 (tt0) cc_final: 0.8290 (tm-30) REVERT: B 738 CYS cc_start: 0.7948 (t) cc_final: 0.7686 (t) REVERT: B 759 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: B 969 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8465 (mtpp) REVERT: B 1002 GLN cc_start: 0.8548 (tm-30) cc_final: 0.7941 (pp30) REVERT: C 100 ILE cc_start: 0.8723 (mm) cc_final: 0.8512 (mm) REVERT: C 134 GLN cc_start: 0.9061 (tp40) cc_final: 0.8548 (mm110) REVERT: C 200 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.6178 (t80) REVERT: C 242 LEU cc_start: 0.7549 (mt) cc_final: 0.7260 (mt) REVERT: C 271 GLN cc_start: 0.8945 (mp10) cc_final: 0.8707 (mp10) REVERT: C 302 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8972 (p) REVERT: C 324 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: C 353 TRP cc_start: 0.8208 (p-90) cc_final: 0.7750 (p-90) REVERT: C 421 TYR cc_start: 0.8257 (m-10) cc_final: 0.7979 (m-10) REVERT: C 586 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: C 749 CYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6511 (t) REVERT: C 761 THR cc_start: 0.8742 (m) cc_final: 0.8439 (p) REVERT: C 859 THR cc_start: 0.9136 (m) cc_final: 0.8739 (p) REVERT: C 933 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7993 (mtpt) REVERT: C 957 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 960 ASN cc_start: 0.8861 (t0) cc_final: 0.8661 (m-40) REVERT: C 983 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.6895 (tpm170) REVERT: C 1142 GLN cc_start: 0.8743 (tp40) cc_final: 0.8081 (tm-30) outliers start: 68 outliers final: 25 residues processed: 240 average time/residue: 1.0450 time to fit residues: 298.8871 Evaluate side-chains 197 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 208 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN A1002 GLN A1005 GLN B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 388 ASN C 450 ASN C 606 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.131079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080365 restraints weight = 44721.395| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.95 r_work: 0.3010 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22527 Z= 0.207 Angle : 0.612 10.463 30752 Z= 0.305 Chirality : 0.046 0.268 3659 Planarity : 0.004 0.063 3857 Dihedral : 5.153 52.769 4089 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.57 % Allowed : 13.79 % Favored : 83.64 % 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: 0.26 (0.16), residues: 2645 helix: 1.76 (0.20), residues: 640 sheet: 0.08 (0.20), residues: 603 loop : -0.51 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.027 0.002 PHE A 981 TYR 0.020 0.001 TYR B1067 ARG 0.007 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 40) link_NAG-ASN : angle 2.46342 ( 120) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.04886 ( 54) hydrogen bonds : bond 0.04004 ( 951) hydrogen bonds : angle 5.74827 ( 2808) SS BOND : bond 0.00333 ( 34) SS BOND : angle 1.64148 ( 68) covalent geometry : bond 0.00481 (22435) covalent geometry : angle 0.58765 (30510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7227 (t0) cc_final: 0.6979 (t0) REVERT: A 54 LEU cc_start: 0.8698 (mt) cc_final: 0.8422 (mm) REVERT: A 200 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: A 269 TYR cc_start: 0.7860 (m-80) cc_final: 0.7001 (m-80) REVERT: A 314 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8317 (tp-100) REVERT: A 560 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 755 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: A 773 GLU cc_start: 0.8720 (tt0) cc_final: 0.8446 (tt0) REVERT: A 964 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8675 (mttt) REVERT: A 979 ASP cc_start: 0.7973 (t0) cc_final: 0.7697 (t0) REVERT: A 985 ASP cc_start: 0.7734 (p0) cc_final: 0.7459 (p0) REVERT: A 988 GLU cc_start: 0.8630 (mp0) cc_final: 0.8209 (mp0) REVERT: A 1092 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: B 238 PHE cc_start: 0.6906 (p90) cc_final: 0.6433 (p90) REVERT: B 314 GLN cc_start: 0.8583 (tt0) cc_final: 0.8126 (tm-30) REVERT: B 738 CYS cc_start: 0.7586 (t) cc_final: 0.7347 (t) REVERT: B 752 LEU cc_start: 0.8839 (tp) cc_final: 0.8070 (tp) REVERT: B 755 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7572 (mp10) REVERT: B 759 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 1002 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8217 (pp30) REVERT: C 54 LEU cc_start: 0.8504 (pp) cc_final: 0.8283 (tt) REVERT: C 100 ILE cc_start: 0.8681 (mm) cc_final: 0.8464 (mm) REVERT: C 134 GLN cc_start: 0.9088 (tp40) cc_final: 0.8514 (mm110) REVERT: C 135 PHE cc_start: 0.7591 (m-80) cc_final: 0.7380 (m-80) REVERT: C 200 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6522 (t80) REVERT: C 242 LEU cc_start: 0.7492 (mt) cc_final: 0.7180 (mt) REVERT: C 302 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8963 (p) REVERT: C 324 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: C 353 TRP cc_start: 0.8193 (p-90) cc_final: 0.7673 (p-90) REVERT: C 421 TYR cc_start: 0.8228 (m-10) cc_final: 0.8005 (m-10) REVERT: C 749 CYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6529 (t) REVERT: C 761 THR cc_start: 0.8649 (m) cc_final: 0.8301 (p) REVERT: C 859 THR cc_start: 0.9101 (m) cc_final: 0.8797 (p) REVERT: C 933 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8001 (mtpt) REVERT: C 990 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7560 (mt-10) REVERT: C 1142 GLN cc_start: 0.8792 (tp40) cc_final: 0.8106 (tm-30) outliers start: 61 outliers final: 26 residues processed: 211 average time/residue: 1.0044 time to fit residues: 252.2080 Evaluate side-chains 194 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 162 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 166 optimal weight: 40.0000 chunk 266 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 184 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 238 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B 66 HIS B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.131751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.081508 restraints weight = 44594.752| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.95 r_work: 0.3047 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 22527 Z= 0.145 Angle : 0.583 10.153 30752 Z= 0.290 Chirality : 0.045 0.273 3659 Planarity : 0.004 0.051 3857 Dihedral : 4.918 53.266 4089 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.19 % Allowed : 14.21 % Favored : 83.60 % 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: 0.43 (0.16), residues: 2645 helix: 1.91 (0.20), residues: 640 sheet: 0.27 (0.20), residues: 612 loop : -0.45 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.027 0.001 PHE A 133 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 40) link_NAG-ASN : angle 2.36241 ( 120) link_BETA1-4 : bond 0.00318 ( 18) link_BETA1-4 : angle 0.97368 ( 54) hydrogen bonds : bond 0.03725 ( 951) hydrogen bonds : angle 5.59339 ( 2808) SS BOND : bond 0.00195 ( 34) SS BOND : angle 1.46410 ( 68) covalent geometry : bond 0.00333 (22435) covalent geometry : angle 0.56096 (30510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8712 (mt) cc_final: 0.8416 (mm) REVERT: A 102 ARG cc_start: 0.7003 (mmp80) cc_final: 0.6661 (tpp-160) REVERT: A 200 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.5635 (m-80) REVERT: A 201 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6377 (t80) REVERT: A 269 TYR cc_start: 0.7935 (m-80) cc_final: 0.7080 (m-80) REVERT: A 314 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8278 (tp-100) REVERT: A 560 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 773 GLU cc_start: 0.8654 (tt0) cc_final: 0.8198 (tt0) REVERT: A 964 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8663 (mttt) REVERT: A 979 ASP cc_start: 0.7976 (t0) cc_final: 0.7710 (t0) REVERT: A 981 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: A 985 ASP cc_start: 0.7731 (p0) cc_final: 0.7435 (p0) REVERT: A 988 GLU cc_start: 0.8671 (mp0) cc_final: 0.8206 (mp0) REVERT: A 1092 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8363 (mt-10) REVERT: B 55 PHE cc_start: 0.7477 (m-80) cc_final: 0.7076 (m-80) REVERT: B 237 ARG cc_start: 0.8771 (mtp180) cc_final: 0.8415 (mtm110) REVERT: B 238 PHE cc_start: 0.6856 (p90) cc_final: 0.6529 (p90) REVERT: B 314 GLN cc_start: 0.8534 (tt0) cc_final: 0.8118 (tm-30) REVERT: B 738 CYS cc_start: 0.7519 (t) cc_final: 0.7316 (t) REVERT: B 752 LEU cc_start: 0.8940 (tp) cc_final: 0.8147 (tp) REVERT: B 755 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7547 (mp10) REVERT: B 759 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: B 934 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8316 (mp) REVERT: B 1002 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8172 (pp30) REVERT: C 100 ILE cc_start: 0.8664 (mm) cc_final: 0.8440 (mm) REVERT: C 134 GLN cc_start: 0.9090 (tp40) cc_final: 0.8484 (mm110) REVERT: C 200 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6527 (t80) REVERT: C 242 LEU cc_start: 0.7411 (mt) cc_final: 0.7114 (mt) REVERT: C 302 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8962 (p) REVERT: C 324 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: C 353 TRP cc_start: 0.8152 (p-90) cc_final: 0.7703 (p-90) REVERT: C 421 TYR cc_start: 0.8219 (m-10) cc_final: 0.8003 (m-10) REVERT: C 749 CYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6515 (t) REVERT: C 761 THR cc_start: 0.8634 (m) cc_final: 0.8282 (p) REVERT: C 859 THR cc_start: 0.9087 (m) cc_final: 0.8824 (p) REVERT: C 990 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7422 (mt-10) REVERT: C 1142 GLN cc_start: 0.8803 (tp40) cc_final: 0.8111 (tm-30) outliers start: 52 outliers final: 25 residues processed: 207 average time/residue: 1.0132 time to fit residues: 249.7871 Evaluate side-chains 194 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B 66 HIS B 125 ASN B1005 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.131096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080708 restraints weight = 44838.220| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.94 r_work: 0.3049 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22527 Z= 0.185 Angle : 0.601 9.877 30752 Z= 0.302 Chirality : 0.046 0.274 3659 Planarity : 0.004 0.056 3857 Dihedral : 4.893 52.051 4089 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.27 % Allowed : 14.47 % Favored : 83.26 % 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: 0.42 (0.16), residues: 2645 helix: 1.91 (0.20), residues: 640 sheet: 0.24 (0.20), residues: 632 loop : -0.45 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.036 0.001 PHE C 392 TYR 0.020 0.001 TYR B1067 ARG 0.009 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 40) link_NAG-ASN : angle 2.36156 ( 120) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.00271 ( 54) hydrogen bonds : bond 0.03818 ( 951) hydrogen bonds : angle 5.61858 ( 2808) SS BOND : bond 0.00199 ( 34) SS BOND : angle 1.40758 ( 68) covalent geometry : bond 0.00427 (22435) covalent geometry : angle 0.57926 (30510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6997 (mmp80) cc_final: 0.6538 (tpp-160) REVERT: A 200 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5670 (m-80) REVERT: A 201 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6414 (t80) REVERT: A 314 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8277 (tp-100) REVERT: A 773 GLU cc_start: 0.8688 (tt0) cc_final: 0.8228 (tt0) REVERT: A 979 ASP cc_start: 0.7996 (t0) cc_final: 0.7712 (t0) REVERT: A 985 ASP cc_start: 0.7774 (p0) cc_final: 0.7532 (p0) REVERT: A 988 GLU cc_start: 0.8673 (mp0) cc_final: 0.8196 (mp0) REVERT: B 55 PHE cc_start: 0.7447 (m-80) cc_final: 0.7063 (m-80) REVERT: B 237 ARG cc_start: 0.8785 (mtp180) cc_final: 0.8442 (mtm110) REVERT: B 238 PHE cc_start: 0.6893 (p90) cc_final: 0.6574 (p90) REVERT: B 314 GLN cc_start: 0.8527 (tt0) cc_final: 0.8125 (tm-30) REVERT: B 738 CYS cc_start: 0.7625 (t) cc_final: 0.7406 (t) REVERT: B 752 LEU cc_start: 0.8957 (tp) cc_final: 0.8166 (tp) REVERT: B 755 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7514 (mp10) REVERT: B 759 PHE cc_start: 0.8307 (m-80) cc_final: 0.8075 (m-80) REVERT: B 934 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 1002 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8184 (pp30) REVERT: C 63 THR cc_start: 0.6098 (OUTLIER) cc_final: 0.5781 (t) REVERT: C 100 ILE cc_start: 0.8708 (mm) cc_final: 0.8482 (mm) REVERT: C 134 GLN cc_start: 0.9085 (tp40) cc_final: 0.8447 (mm110) REVERT: C 135 PHE cc_start: 0.7477 (m-80) cc_final: 0.7196 (m-80) REVERT: C 200 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.6665 (t80) REVERT: C 242 LEU cc_start: 0.7600 (mt) cc_final: 0.7267 (mt) REVERT: C 302 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8988 (p) REVERT: C 324 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: C 353 TRP cc_start: 0.8136 (p-90) cc_final: 0.7630 (p-90) REVERT: C 421 TYR cc_start: 0.8252 (m-10) cc_final: 0.8033 (m-10) REVERT: C 749 CYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6532 (t) REVERT: C 761 THR cc_start: 0.8667 (m) cc_final: 0.8325 (p) REVERT: C 859 THR cc_start: 0.9099 (m) cc_final: 0.8821 (p) REVERT: C 933 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8104 (mtpt) REVERT: C 990 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 1142 GLN cc_start: 0.8824 (tp40) cc_final: 0.8141 (tm-30) outliers start: 54 outliers final: 28 residues processed: 201 average time/residue: 0.9935 time to fit residues: 239.1870 Evaluate side-chains 191 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 237 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 221 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 87 ASN A 762 GLN B 66 HIS B1005 GLN C 613 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.131232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.080763 restraints weight = 44729.792| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.94 r_work: 0.3039 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22527 Z= 0.164 Angle : 0.599 11.281 30752 Z= 0.299 Chirality : 0.045 0.278 3659 Planarity : 0.004 0.051 3857 Dihedral : 4.847 52.685 4089 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.89 % Allowed : 14.93 % Favored : 83.18 % 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: 0.40 (0.16), residues: 2645 helix: 1.92 (0.21), residues: 635 sheet: 0.22 (0.20), residues: 596 loop : -0.45 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.038 0.001 PHE A 981 TYR 0.020 0.001 TYR B1067 ARG 0.012 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 40) link_NAG-ASN : angle 2.32453 ( 120) link_BETA1-4 : bond 0.00315 ( 18) link_BETA1-4 : angle 0.97148 ( 54) hydrogen bonds : bond 0.03755 ( 951) hydrogen bonds : angle 5.59673 ( 2808) SS BOND : bond 0.00209 ( 34) SS BOND : angle 1.28847 ( 68) covalent geometry : bond 0.00380 (22435) covalent geometry : angle 0.57915 (30510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6969 (mmp80) cc_final: 0.6538 (tpp-160) REVERT: A 200 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: A 201 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 314 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8258 (tp-100) REVERT: A 560 LEU cc_start: 0.8703 (mm) cc_final: 0.8321 (mp) REVERT: A 773 GLU cc_start: 0.8631 (tt0) cc_final: 0.8183 (tt0) REVERT: A 964 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8657 (mtmt) REVERT: A 979 ASP cc_start: 0.7932 (t0) cc_final: 0.7644 (t0) REVERT: A 985 ASP cc_start: 0.7783 (p0) cc_final: 0.7502 (p0) REVERT: A 988 GLU cc_start: 0.8682 (mp0) cc_final: 0.8200 (mp0) REVERT: A 1092 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: B 55 PHE cc_start: 0.7431 (m-80) cc_final: 0.7045 (m-80) REVERT: B 237 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8440 (mtm110) REVERT: B 238 PHE cc_start: 0.6928 (p90) cc_final: 0.6636 (p90) REVERT: B 314 GLN cc_start: 0.8505 (tt0) cc_final: 0.8119 (tm-30) REVERT: B 752 LEU cc_start: 0.8959 (tp) cc_final: 0.8159 (tp) REVERT: B 755 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7612 (mp10) REVERT: B 759 PHE cc_start: 0.8301 (m-80) cc_final: 0.8067 (m-80) REVERT: B 934 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 1002 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8163 (pp30) REVERT: C 63 THR cc_start: 0.6052 (OUTLIER) cc_final: 0.5688 (p) REVERT: C 100 ILE cc_start: 0.8739 (mm) cc_final: 0.8522 (mm) REVERT: C 134 GLN cc_start: 0.9101 (tp40) cc_final: 0.8412 (mm110) REVERT: C 135 PHE cc_start: 0.7384 (m-80) cc_final: 0.7118 (m-80) REVERT: C 200 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6705 (t80) REVERT: C 242 LEU cc_start: 0.7755 (mt) cc_final: 0.7453 (mt) REVERT: C 302 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8986 (p) REVERT: C 324 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: C 353 TRP cc_start: 0.8153 (p-90) cc_final: 0.7647 (p-90) REVERT: C 421 TYR cc_start: 0.8231 (m-10) cc_final: 0.8003 (m-10) REVERT: C 761 THR cc_start: 0.8669 (m) cc_final: 0.8323 (p) REVERT: C 859 THR cc_start: 0.9086 (m) cc_final: 0.8813 (p) REVERT: C 933 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8069 (mtpt) REVERT: C 957 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: C 990 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 1142 GLN cc_start: 0.8798 (tp40) cc_final: 0.8197 (tm-30) outliers start: 45 outliers final: 23 residues processed: 189 average time/residue: 1.1662 time to fit residues: 261.0657 Evaluate side-chains 181 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 19 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 238 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 66 HIS B 957 GLN B1005 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.131430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081242 restraints weight = 44720.994| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.94 r_work: 0.3048 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22527 Z= 0.148 Angle : 0.594 11.709 30752 Z= 0.296 Chirality : 0.045 0.280 3659 Planarity : 0.004 0.053 3857 Dihedral : 4.804 52.822 4089 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.77 % Allowed : 15.35 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2645 helix: 1.93 (0.21), residues: 635 sheet: 0.17 (0.20), residues: 601 loop : -0.37 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.026 0.001 PHE A 981 TYR 0.020 0.001 TYR B1067 ARG 0.010 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 40) link_NAG-ASN : angle 2.29846 ( 120) link_BETA1-4 : bond 0.00289 ( 18) link_BETA1-4 : angle 0.94614 ( 54) hydrogen bonds : bond 0.03700 ( 951) hydrogen bonds : angle 5.57444 ( 2808) SS BOND : bond 0.00375 ( 34) SS BOND : angle 1.37741 ( 68) covalent geometry : bond 0.00342 (22435) covalent geometry : angle 0.57326 (30510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6964 (mmp80) cc_final: 0.6547 (tpp-160) REVERT: A 200 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.5708 (m-80) REVERT: A 201 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6414 (t80) REVERT: A 269 TYR cc_start: 0.7373 (m-10) cc_final: 0.6885 (m-80) REVERT: A 314 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8247 (tp-100) REVERT: A 560 LEU cc_start: 0.8685 (mm) cc_final: 0.8293 (mp) REVERT: A 773 GLU cc_start: 0.8598 (tt0) cc_final: 0.8149 (tt0) REVERT: A 979 ASP cc_start: 0.7916 (t0) cc_final: 0.7641 (t0) REVERT: A 985 ASP cc_start: 0.7778 (p0) cc_final: 0.7375 (p0) REVERT: A 988 GLU cc_start: 0.8678 (mp0) cc_final: 0.8185 (mp0) REVERT: A 1092 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: B 55 PHE cc_start: 0.7433 (m-80) cc_final: 0.7073 (m-80) REVERT: B 237 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8432 (mtm110) REVERT: B 238 PHE cc_start: 0.6928 (p90) cc_final: 0.6630 (p90) REVERT: B 314 GLN cc_start: 0.8425 (tt0) cc_final: 0.8027 (tm-30) REVERT: B 752 LEU cc_start: 0.8949 (tp) cc_final: 0.8195 (tp) REVERT: B 755 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7585 (mp10) REVERT: B 759 PHE cc_start: 0.8325 (m-80) cc_final: 0.8062 (m-80) REVERT: B 934 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (mp) REVERT: B 1002 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8155 (pp30) REVERT: C 63 THR cc_start: 0.6005 (OUTLIER) cc_final: 0.5641 (p) REVERT: C 100 ILE cc_start: 0.8752 (mm) cc_final: 0.8536 (mm) REVERT: C 134 GLN cc_start: 0.9109 (tp40) cc_final: 0.8399 (mm110) REVERT: C 135 PHE cc_start: 0.7427 (m-80) cc_final: 0.7166 (m-80) REVERT: C 200 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6690 (t80) REVERT: C 242 LEU cc_start: 0.7737 (mt) cc_final: 0.7421 (mt) REVERT: C 302 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8986 (p) REVERT: C 324 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: C 353 TRP cc_start: 0.8100 (p-90) cc_final: 0.7599 (p-90) REVERT: C 421 TYR cc_start: 0.8230 (m-10) cc_final: 0.8003 (m-10) REVERT: C 761 THR cc_start: 0.8669 (m) cc_final: 0.8326 (p) REVERT: C 859 THR cc_start: 0.9085 (m) cc_final: 0.8825 (p) REVERT: C 933 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8059 (mtpt) REVERT: C 973 ILE cc_start: 0.9299 (pt) cc_final: 0.9085 (pp) REVERT: C 990 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 1142 GLN cc_start: 0.8802 (tp40) cc_final: 0.8200 (tm-30) outliers start: 42 outliers final: 24 residues processed: 184 average time/residue: 1.0311 time to fit residues: 226.1733 Evaluate side-chains 183 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 75 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 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 66 HIS A 762 GLN A 957 GLN B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.129909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.079178 restraints weight = 44868.544| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.94 r_work: 0.2982 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 22527 Z= 0.234 Angle : 0.640 10.853 30752 Z= 0.319 Chirality : 0.047 0.278 3659 Planarity : 0.004 0.045 3857 Dihedral : 4.929 51.306 4089 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.60 % Allowed : 15.60 % Favored : 82.80 % 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: 0.35 (0.16), residues: 2645 helix: 1.81 (0.20), residues: 640 sheet: 0.19 (0.20), residues: 604 loop : -0.46 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.005 0.001 HIS C1048 PHE 0.033 0.002 PHE A 133 TYR 0.021 0.002 TYR B1067 ARG 0.011 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 40) link_NAG-ASN : angle 2.37531 ( 120) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.01986 ( 54) hydrogen bonds : bond 0.04056 ( 951) hydrogen bonds : angle 5.74790 ( 2808) SS BOND : bond 0.00554 ( 34) SS BOND : angle 1.56075 ( 68) covalent geometry : bond 0.00546 (22435) covalent geometry : angle 0.61879 (30510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21415.27 seconds wall clock time: 372 minutes 4.97 seconds (22324.97 seconds total)