Starting phenix.real_space_refine on Sat Jun 21 14:42:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uir_42302/06_2025/8uir_42302.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uir_42302/06_2025/8uir_42302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uir_42302/06_2025/8uir_42302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uir_42302/06_2025/8uir_42302.map" model { file = "/net/cci-nas-00/data/ceres_data/8uir_42302/06_2025/8uir_42302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uir_42302/06_2025/8uir_42302.cif" } resolution = 3.2 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= -0.001 sd= 0.050 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 114 5.16 5 C 15861 2.51 5 N 4074 2.21 5 O 4830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 24879 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.43, per 1000 atoms: 0.62 Number of scatterers: 24879 At special positions: 0 Unit cell: (139.32, 132.84, 174.96, 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 114 16.00 O 4830 8.00 N 4074 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 A 840 " - pdb=" SG CYS A 851 " distance=2.04 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 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 B 840 " - pdb=" SG CYS B 851 " 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 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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=2, 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN C 234 " " NAG C1301 " - " ASN A 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.5 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 51 sheets defined 24.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.048A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.815A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.050A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.389A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.619A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.951A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.850A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.789A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.576A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.049A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.584A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.662A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.588A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.049A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.788A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.853A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.684A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.668A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.073A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.667A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.531A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.741A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.634A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 947 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 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.674A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.054A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.769A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.082A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.727A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.547A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.709A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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 removed outlier: 3.730A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.535A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.080A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.594A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.578A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.218A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.640A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.512A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.881A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.674A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.668A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.639A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.447A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.028A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.523A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.679A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.923A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.459A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.545A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.820A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.177A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.498A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.633A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.435A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.607A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.197A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.898A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.662A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.202A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.586A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.603A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.535A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.190A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.142A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.428A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 928 hydrogen bonds defined for protein. 2544 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: 13.28 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7875 1.35 - 1.47: 6567 1.47 - 1.60: 10845 1.60 - 1.73: 0 1.73 - 1.86: 141 Bond restraints: 25428 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 25423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 34050 2.51 - 5.03: 474 5.03 - 7.54: 43 7.54 - 10.05: 12 10.05 - 12.57: 5 Bond angle restraints: 34584 Sorted by residual: angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 122.46 130.56 -8.10 1.41e+00 5.03e-01 3.30e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ASN C 87 " pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta sigma weight residual 122.46 129.30 -6.84 1.41e+00 5.03e-01 2.35e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 117.02 -4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" N GLY C 648 " pdb=" CA GLY C 648 " pdb=" C GLY C 648 " ideal model delta sigma weight residual 112.04 108.11 3.93 1.02e+00 9.61e-01 1.49e+01 ... (remaining 34579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14178 17.92 - 35.83: 1294 35.83 - 53.75: 235 53.75 - 71.67: 70 71.67 - 89.59: 15 Dihedral angle restraints: 15792 sinusoidal: 6759 harmonic: 9033 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -147.84 61.84 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 145.02 34.98 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -27.01 -58.99 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3552 0.083 - 0.167: 504 0.167 - 0.250: 12 0.250 - 0.334: 4 0.334 - 0.417: 5 Chirality restraints: 4077 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C2 NAG B1310 " pdb=" C1 NAG B1310 " pdb=" C3 NAG B1310 " pdb=" N2 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 4074 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.006 2.00e-02 2.50e+03 4.00e-02 2.00e+01 pdb=" CG ASN A 343 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 561 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A1143 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.040 5.00e-02 4.00e+02 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7299 2.83 - 3.34: 19517 3.34 - 3.86: 39699 3.86 - 4.38: 44163 4.38 - 4.90: 80310 Nonbonded interactions: 190988 Sorted by model distance: nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.307 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.315 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.332 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.342 3.040 nonbonded pdb=" NH2 ARG B 995 " pdb=" OD2 ASP C 994 " model vdw 2.344 3.120 ... (remaining 190983 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 24 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 24 through 1147 or resid 1301 through 1309)) } 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' } 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: 2.570 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 60.790 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.180 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:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.062 25520 Z= 0.207 Angle : 0.752 13.261 34812 Z= 0.375 Chirality : 0.053 0.417 4077 Planarity : 0.006 0.084 4404 Dihedral : 14.126 89.586 9852 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.14), residues: 3057 helix: -0.48 (0.17), residues: 672 sheet: 0.50 (0.22), residues: 561 loop : -1.51 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.007 0.001 HIS C 66 PHE 0.033 0.001 PHE C 592 TYR 0.028 0.001 TYR A 837 ARG 0.011 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 39) link_NAG-ASN : angle 3.75118 ( 117) link_BETA1-4 : bond 0.01442 ( 9) link_BETA1-4 : angle 4.83375 ( 27) hydrogen bonds : bond 0.20599 ( 916) hydrogen bonds : angle 7.93131 ( 2544) SS BOND : bond 0.00504 ( 42) SS BOND : angle 1.56142 ( 84) covalent geometry : bond 0.00415 (25428) covalent geometry : angle 0.70509 (34584) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7016 (t80) cc_final: 0.6532 (t80) REVERT: A 200 TYR cc_start: 0.5658 (t80) cc_final: 0.5251 (t80) REVERT: A 641 ASN cc_start: 0.7284 (m110) cc_final: 0.6924 (m110) REVERT: B 339 HIS cc_start: 0.7030 (t-90) cc_final: 0.6667 (t70) REVERT: B 568 ASP cc_start: 0.7477 (t0) cc_final: 0.7037 (t0) REVERT: C 177 MET cc_start: 0.6190 (pmm) cc_final: 0.5967 (pmm) REVERT: C 493 GLN cc_start: 0.8067 (tt0) cc_final: 0.7807 (tt0) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3416 time to fit residues: 124.9475 Evaluate side-chains 188 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN A 935 GLN B 207 HIS B 339 HIS B 394 ASN B1106 GLN C 66 HIS C 613 GLN C 901 GLN C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130004 restraints weight = 27374.892| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.07 r_work: 0.2991 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25520 Z= 0.118 Angle : 0.552 10.138 34812 Z= 0.274 Chirality : 0.045 0.379 4077 Planarity : 0.004 0.056 4404 Dihedral : 7.246 59.811 4326 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.45 % Allowed : 5.05 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3057 helix: 1.23 (0.20), residues: 675 sheet: 0.65 (0.21), residues: 606 loop : -1.37 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE A 906 TYR 0.012 0.001 TYR A1067 ARG 0.002 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 39) link_NAG-ASN : angle 2.53977 ( 117) link_BETA1-4 : bond 0.00963 ( 9) link_BETA1-4 : angle 2.95581 ( 27) hydrogen bonds : bond 0.04780 ( 916) hydrogen bonds : angle 5.46818 ( 2544) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.20910 ( 84) covalent geometry : bond 0.00271 (25428) covalent geometry : angle 0.52376 (34584) Misc. bond : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7437 (t80) cc_final: 0.6890 (t80) REVERT: A 200 TYR cc_start: 0.5560 (t80) cc_final: 0.5162 (t80) REVERT: A 574 ASP cc_start: 0.8451 (t0) cc_final: 0.8215 (t0) REVERT: A 641 ASN cc_start: 0.7018 (m110) cc_final: 0.6677 (m110) REVERT: B 339 HIS cc_start: 0.7165 (t70) cc_final: 0.6937 (t70) REVERT: B 578 ASP cc_start: 0.7909 (t0) cc_final: 0.7642 (t0) REVERT: C 177 MET cc_start: 0.6236 (pmm) cc_final: 0.5921 (pmm) REVERT: C 388 ASN cc_start: 0.8902 (m-40) cc_final: 0.8685 (m-40) REVERT: C 448 ASN cc_start: 0.7527 (t0) cc_final: 0.7132 (t0) REVERT: C 493 GLN cc_start: 0.7561 (tt0) cc_final: 0.7350 (tt0) outliers start: 12 outliers final: 8 residues processed: 224 average time/residue: 0.3681 time to fit residues: 133.6916 Evaluate side-chains 200 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 266 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A 919 ASN B 394 ASN B 607 GLN B1010 GLN B1106 GLN C 66 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 405 ASN C 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.159495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109712 restraints weight = 28178.067| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.59 r_work: 0.2876 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 25520 Z= 0.303 Angle : 0.729 10.985 34812 Z= 0.365 Chirality : 0.052 0.370 4077 Planarity : 0.005 0.057 4404 Dihedral : 7.349 59.959 4326 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.19 % Allowed : 8.09 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3057 helix: 1.33 (0.21), residues: 648 sheet: 0.37 (0.21), residues: 606 loop : -1.46 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.009 0.002 HIS B1048 PHE 0.040 0.002 PHE B 906 TYR 0.020 0.002 TYR A 279 ARG 0.005 0.001 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 39) link_NAG-ASN : angle 2.99579 ( 117) link_BETA1-4 : bond 0.00930 ( 9) link_BETA1-4 : angle 3.03592 ( 27) hydrogen bonds : bond 0.07264 ( 916) hydrogen bonds : angle 5.49567 ( 2544) SS BOND : bond 0.00657 ( 42) SS BOND : angle 1.81814 ( 84) covalent geometry : bond 0.00767 (25428) covalent geometry : angle 0.69962 (34584) Misc. bond : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.6958 (tpp-160) REVERT: A 170 TYR cc_start: 0.7809 (t80) cc_final: 0.6997 (t80) REVERT: A 454 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.7027 (ttm-80) REVERT: A 492 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7973 (tp) REVERT: A 498 ARG cc_start: 0.6245 (mmt-90) cc_final: 0.5810 (mpt90) REVERT: A 641 ASN cc_start: 0.7141 (m110) cc_final: 0.6794 (m110) REVERT: B 339 HIS cc_start: 0.7412 (t70) cc_final: 0.7070 (t-90) REVERT: B 578 ASP cc_start: 0.8346 (t0) cc_final: 0.8035 (t0) REVERT: B 740 MET cc_start: 0.9122 (mmm) cc_final: 0.8228 (ttm) REVERT: C 316 SER cc_start: 0.9090 (t) cc_final: 0.8720 (p) REVERT: C 388 ASN cc_start: 0.8995 (m-40) cc_final: 0.8710 (m-40) REVERT: C 448 ASN cc_start: 0.7983 (t0) cc_final: 0.7444 (t0) REVERT: C 814 LYS cc_start: 0.8536 (mptt) cc_final: 0.7523 (mtpp) REVERT: C 1092 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8098 (mt-10) outliers start: 32 outliers final: 24 residues processed: 239 average time/residue: 0.3633 time to fit residues: 140.0838 Evaluate side-chains 220 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 26 GLN B 394 ASN B 901 GLN C 207 HIS C 339 HIS C 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.166766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117955 restraints weight = 27708.862| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.53 r_work: 0.2914 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25520 Z= 0.125 Angle : 0.568 10.209 34812 Z= 0.279 Chirality : 0.046 0.427 4077 Planarity : 0.004 0.054 4404 Dihedral : 6.948 59.492 4326 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.04 % Allowed : 10.32 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.34 (0.15), residues: 3057 helix: 1.84 (0.21), residues: 648 sheet: 0.43 (0.21), residues: 600 loop : -1.31 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE B 377 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 39) link_NAG-ASN : angle 2.74000 ( 117) link_BETA1-4 : bond 0.01035 ( 9) link_BETA1-4 : angle 2.88718 ( 27) hydrogen bonds : bond 0.05017 ( 916) hydrogen bonds : angle 5.11365 ( 2544) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.41021 ( 84) covalent geometry : bond 0.00288 (25428) covalent geometry : angle 0.53633 (34584) Misc. bond : bond 0.00228 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7189 (tpp-160) cc_final: 0.6731 (tpp-160) REVERT: A 170 TYR cc_start: 0.7636 (t80) cc_final: 0.6898 (t80) REVERT: A 392 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: A 492 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8109 (tp) REVERT: A 498 ARG cc_start: 0.6052 (mmt-90) cc_final: 0.5691 (mpt90) REVERT: A 574 ASP cc_start: 0.8493 (t0) cc_final: 0.8292 (t0) REVERT: A 641 ASN cc_start: 0.6926 (m110) cc_final: 0.6623 (m110) REVERT: B 339 HIS cc_start: 0.7253 (t70) cc_final: 0.7005 (t-90) REVERT: B 578 ASP cc_start: 0.8208 (t0) cc_final: 0.7918 (t0) REVERT: B 740 MET cc_start: 0.8951 (mmm) cc_final: 0.8148 (ttm) REVERT: C 368 ILE cc_start: 0.8491 (mt) cc_final: 0.8218 (mm) REVERT: C 448 ASN cc_start: 0.7905 (t0) cc_final: 0.7505 (t0) REVERT: C 814 LYS cc_start: 0.8413 (mptt) cc_final: 0.7593 (mmmt) REVERT: C 1092 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7914 (mt-10) outliers start: 28 outliers final: 14 residues processed: 230 average time/residue: 0.3945 time to fit residues: 149.4186 Evaluate side-chains 217 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 158 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 281 optimal weight: 0.0020 chunk 159 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN C 207 HIS C 314 GLN C 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.167011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124419 restraints weight = 27637.186| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.37 r_work: 0.2911 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25520 Z= 0.125 Angle : 0.548 10.335 34812 Z= 0.269 Chirality : 0.045 0.348 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.656 59.343 4326 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.48 % Allowed : 10.62 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.19 (0.15), residues: 3057 helix: 2.06 (0.21), residues: 648 sheet: 0.37 (0.21), residues: 624 loop : -1.21 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.018 0.001 PHE B 92 TYR 0.015 0.001 TYR A1067 ARG 0.005 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 39) link_NAG-ASN : angle 2.59421 ( 117) link_BETA1-4 : bond 0.01017 ( 9) link_BETA1-4 : angle 2.82980 ( 27) hydrogen bonds : bond 0.04741 ( 916) hydrogen bonds : angle 4.93560 ( 2544) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.35333 ( 84) covalent geometry : bond 0.00296 (25428) covalent geometry : angle 0.51898 (34584) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7655 (t80) cc_final: 0.6888 (t80) REVERT: A 492 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 498 ARG cc_start: 0.6089 (mmt-90) cc_final: 0.5643 (mpt90) REVERT: A 568 ASP cc_start: 0.7227 (t0) cc_final: 0.6965 (t0) REVERT: A 641 ASN cc_start: 0.6975 (m110) cc_final: 0.6676 (m110) REVERT: B 106 PHE cc_start: 0.6220 (m-80) cc_final: 0.5988 (m-80) REVERT: B 200 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.4225 (m-80) REVERT: B 339 HIS cc_start: 0.7321 (t70) cc_final: 0.7028 (t-90) REVERT: B 574 ASP cc_start: 0.8341 (t0) cc_final: 0.7814 (t0) REVERT: B 578 ASP cc_start: 0.8226 (t0) cc_final: 0.7924 (t0) REVERT: B 740 MET cc_start: 0.8955 (mmm) cc_final: 0.8152 (ttm) REVERT: B 854 LYS cc_start: 0.7511 (tptt) cc_final: 0.7215 (tptt) REVERT: C 368 ILE cc_start: 0.8452 (mt) cc_final: 0.8150 (mm) REVERT: C 448 ASN cc_start: 0.7946 (t0) cc_final: 0.7491 (t0) REVERT: C 814 LYS cc_start: 0.8415 (mptt) cc_final: 0.7542 (mmmt) REVERT: C 935 GLN cc_start: 0.5888 (tt0) cc_final: 0.5655 (tt0) REVERT: C 1092 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8001 (mt-10) outliers start: 40 outliers final: 23 residues processed: 231 average time/residue: 0.3430 time to fit residues: 130.2884 Evaluate side-chains 221 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 45 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 207 optimal weight: 0.2980 chunk 241 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 394 ASN C 66 HIS C 207 HIS C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116422 restraints weight = 27572.784| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.49 r_work: 0.2894 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25520 Z= 0.175 Angle : 0.586 10.825 34812 Z= 0.289 Chirality : 0.047 0.355 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.706 59.230 4326 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.86 % Allowed : 11.25 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.24 (0.15), residues: 3057 helix: 2.01 (0.21), residues: 645 sheet: 0.39 (0.21), residues: 600 loop : -1.23 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 PHE 0.018 0.001 PHE B 377 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 39) link_NAG-ASN : angle 2.63975 ( 117) link_BETA1-4 : bond 0.00988 ( 9) link_BETA1-4 : angle 2.81607 ( 27) hydrogen bonds : bond 0.05309 ( 916) hydrogen bonds : angle 4.98748 ( 2544) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.54840 ( 84) covalent geometry : bond 0.00434 (25428) covalent geometry : angle 0.55708 (34584) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7508 (tpp-160) cc_final: 0.7268 (tpp-160) REVERT: A 170 TYR cc_start: 0.7707 (t80) cc_final: 0.6917 (t80) REVERT: A 392 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: A 492 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7904 (tp) REVERT: A 498 ARG cc_start: 0.6233 (mmt-90) cc_final: 0.5645 (mpt90) REVERT: A 641 ASN cc_start: 0.6963 (m110) cc_final: 0.6679 (m110) REVERT: A 1084 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8197 (t0) REVERT: B 200 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.4029 (m-80) REVERT: B 339 HIS cc_start: 0.7312 (t70) cc_final: 0.7016 (t-90) REVERT: B 377 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6206 (t80) REVERT: B 574 ASP cc_start: 0.8431 (t0) cc_final: 0.8120 (t0) REVERT: B 578 ASP cc_start: 0.8269 (t0) cc_final: 0.7971 (t0) REVERT: B 740 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: B 854 LYS cc_start: 0.7516 (tptt) cc_final: 0.7246 (tptt) REVERT: C 316 SER cc_start: 0.8911 (t) cc_final: 0.8692 (p) REVERT: C 448 ASN cc_start: 0.8040 (t0) cc_final: 0.7519 (t0) REVERT: C 814 LYS cc_start: 0.8458 (mptt) cc_final: 0.7509 (mttm) REVERT: C 1092 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8087 (mt-10) outliers start: 50 outliers final: 30 residues processed: 237 average time/residue: 0.3269 time to fit residues: 126.7665 Evaluate side-chains 232 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 239 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 141 optimal weight: 0.0010 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 87 ASN B 394 ASN C 314 GLN C 339 HIS C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124487 restraints weight = 27513.390| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.26 r_work: 0.2944 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25520 Z= 0.102 Angle : 0.528 11.200 34812 Z= 0.259 Chirality : 0.045 0.354 4077 Planarity : 0.003 0.051 4404 Dihedral : 6.471 59.132 4326 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.41 % Allowed : 11.99 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.07 (0.15), residues: 3057 helix: 2.08 (0.21), residues: 660 sheet: 0.48 (0.21), residues: 600 loop : -1.11 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS B1048 PHE 0.019 0.001 PHE B 92 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 39) link_NAG-ASN : angle 2.54796 ( 117) link_BETA1-4 : bond 0.00985 ( 9) link_BETA1-4 : angle 2.75131 ( 27) hydrogen bonds : bond 0.04268 ( 916) hydrogen bonds : angle 4.80439 ( 2544) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.21215 ( 84) covalent geometry : bond 0.00230 (25428) covalent geometry : angle 0.49890 (34584) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7667 (t80) cc_final: 0.6858 (t80) REVERT: A 392 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: A 492 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 498 ARG cc_start: 0.6169 (mmt-90) cc_final: 0.5943 (mmt180) REVERT: A 568 ASP cc_start: 0.7343 (t0) cc_final: 0.7101 (t0) REVERT: A 641 ASN cc_start: 0.6930 (m110) cc_final: 0.6627 (m110) REVERT: A 1084 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8209 (t0) REVERT: B 200 TYR cc_start: 0.5399 (OUTLIER) cc_final: 0.3919 (m-80) REVERT: B 568 ASP cc_start: 0.7686 (t0) cc_final: 0.7251 (t0) REVERT: B 574 ASP cc_start: 0.8342 (t0) cc_final: 0.7800 (t0) REVERT: B 578 ASP cc_start: 0.8209 (t0) cc_final: 0.7911 (t0) REVERT: B 854 LYS cc_start: 0.7431 (tptt) cc_final: 0.7139 (tptt) REVERT: C 316 SER cc_start: 0.8927 (t) cc_final: 0.8683 (p) REVERT: C 368 ILE cc_start: 0.8739 (mt) cc_final: 0.8463 (mm) REVERT: C 448 ASN cc_start: 0.8052 (t0) cc_final: 0.7541 (t0) REVERT: C 814 LYS cc_start: 0.8381 (mptt) cc_final: 0.7500 (mmmt) REVERT: C 1092 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8006 (mt-10) outliers start: 38 outliers final: 24 residues processed: 231 average time/residue: 0.3425 time to fit residues: 130.5391 Evaluate side-chains 226 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 266 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 394 ASN C 66 HIS C 314 GLN C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.165899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122813 restraints weight = 28415.888| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.11 r_work: 0.2962 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25520 Z= 0.192 Angle : 0.624 21.849 34812 Z= 0.303 Chirality : 0.048 0.612 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.689 59.521 4326 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.48 % Allowed : 12.18 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.21 (0.15), residues: 3057 helix: 2.06 (0.21), residues: 645 sheet: 0.26 (0.20), residues: 627 loop : -1.18 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS B1048 PHE 0.023 0.002 PHE B 168 TYR 0.023 0.001 TYR C 313 ARG 0.003 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 39) link_NAG-ASN : angle 3.49638 ( 117) link_BETA1-4 : bond 0.00974 ( 9) link_BETA1-4 : angle 2.75140 ( 27) hydrogen bonds : bond 0.05541 ( 916) hydrogen bonds : angle 4.98584 ( 2544) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.53003 ( 84) covalent geometry : bond 0.00477 (25428) covalent geometry : angle 0.58186 (34584) Misc. bond : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.7340 (tpp-160) REVERT: A 170 TYR cc_start: 0.7816 (t80) cc_final: 0.7023 (t80) REVERT: A 392 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 492 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 498 ARG cc_start: 0.6392 (mmt-90) cc_final: 0.6164 (mmt180) REVERT: A 568 ASP cc_start: 0.7274 (t0) cc_final: 0.7064 (t0) REVERT: A 641 ASN cc_start: 0.6967 (m110) cc_final: 0.6691 (m110) REVERT: A 916 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 1084 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8318 (t0) REVERT: B 377 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6321 (t80) REVERT: B 574 ASP cc_start: 0.8581 (t0) cc_final: 0.8304 (t0) REVERT: B 578 ASP cc_start: 0.8330 (t0) cc_final: 0.8027 (t0) REVERT: B 740 MET cc_start: 0.9056 (mmm) cc_final: 0.8304 (ttm) REVERT: B 854 LYS cc_start: 0.7529 (tptt) cc_final: 0.7203 (tttp) REVERT: C 448 ASN cc_start: 0.8192 (t0) cc_final: 0.7613 (t0) REVERT: C 814 LYS cc_start: 0.8481 (mptt) cc_final: 0.7478 (mtpp) REVERT: C 1092 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8193 (mt-10) outliers start: 40 outliers final: 27 residues processed: 235 average time/residue: 0.3489 time to fit residues: 134.2879 Evaluate side-chains 231 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 158 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 299 optimal weight: 0.0070 chunk 304 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 73 optimal weight: 0.3980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 394 ASN C 66 HIS C 207 HIS C 314 GLN C 339 HIS C 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.171493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129675 restraints weight = 28121.194| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.63 r_work: 0.3004 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25520 Z= 0.102 Angle : 0.533 11.530 34812 Z= 0.260 Chirality : 0.045 0.355 4077 Planarity : 0.003 0.051 4404 Dihedral : 6.455 59.636 4326 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.41 % Allowed : 12.47 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.00 (0.15), residues: 3057 helix: 2.30 (0.21), residues: 645 sheet: 0.50 (0.21), residues: 573 loop : -1.07 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS B 339 PHE 0.018 0.001 PHE B 92 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 39) link_NAG-ASN : angle 2.82308 ( 117) link_BETA1-4 : bond 0.01001 ( 9) link_BETA1-4 : angle 2.69552 ( 27) hydrogen bonds : bond 0.04210 ( 916) hydrogen bonds : angle 4.78119 ( 2544) SS BOND : bond 0.00407 ( 42) SS BOND : angle 1.22000 ( 84) covalent geometry : bond 0.00227 (25428) covalent geometry : angle 0.49959 (34584) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7473 (tpp-160) cc_final: 0.7194 (tpp-160) REVERT: A 170 TYR cc_start: 0.7760 (t80) cc_final: 0.6978 (t80) REVERT: A 392 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: A 492 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8000 (tp) REVERT: A 568 ASP cc_start: 0.7228 (t0) cc_final: 0.6998 (t0) REVERT: A 641 ASN cc_start: 0.7030 (m110) cc_final: 0.6752 (m110) REVERT: A 916 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 1084 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8234 (t0) REVERT: B 377 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6146 (t80) REVERT: B 568 ASP cc_start: 0.7893 (t0) cc_final: 0.7448 (t0) REVERT: B 574 ASP cc_start: 0.8440 (t0) cc_final: 0.8008 (t0) REVERT: B 578 ASP cc_start: 0.8210 (t0) cc_final: 0.7943 (t0) REVERT: B 854 LYS cc_start: 0.7522 (tptt) cc_final: 0.7247 (tttp) REVERT: C 448 ASN cc_start: 0.8167 (t0) cc_final: 0.7651 (t0) REVERT: C 814 LYS cc_start: 0.8339 (mptt) cc_final: 0.7466 (mmmt) REVERT: C 1092 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8059 (mt-10) outliers start: 38 outliers final: 28 residues processed: 236 average time/residue: 0.3380 time to fit residues: 130.3019 Evaluate side-chains 235 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 178 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 339 HIS B 394 ASN C 66 HIS C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130726 restraints weight = 27992.160| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.33 r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25520 Z= 0.116 Angle : 0.543 11.168 34812 Z= 0.267 Chirality : 0.045 0.357 4077 Planarity : 0.003 0.050 4404 Dihedral : 6.424 59.877 4326 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 12.95 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.04 (0.15), residues: 3057 helix: 2.25 (0.21), residues: 663 sheet: 0.48 (0.21), residues: 603 loop : -1.05 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.026 0.001 PHE B 168 TYR 0.019 0.001 TYR A 904 ARG 0.004 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 39) link_NAG-ASN : angle 2.69198 ( 117) link_BETA1-4 : bond 0.01017 ( 9) link_BETA1-4 : angle 2.67833 ( 27) hydrogen bonds : bond 0.04426 ( 916) hydrogen bonds : angle 4.78917 ( 2544) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.45537 ( 84) covalent geometry : bond 0.00274 (25428) covalent geometry : angle 0.51172 (34584) Misc. bond : bond 0.00112 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7596 (tpp-160) cc_final: 0.7323 (tpp-160) REVERT: A 170 TYR cc_start: 0.7767 (t80) cc_final: 0.7017 (t80) REVERT: A 392 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: A 492 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7858 (tp) REVERT: A 568 ASP cc_start: 0.7174 (t0) cc_final: 0.6965 (t0) REVERT: A 641 ASN cc_start: 0.7023 (m110) cc_final: 0.6748 (m110) REVERT: A 916 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8182 (tp) REVERT: A 1084 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8223 (t0) REVERT: B 377 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6192 (t80) REVERT: B 568 ASP cc_start: 0.7831 (t0) cc_final: 0.7412 (t0) REVERT: B 574 ASP cc_start: 0.8421 (t0) cc_final: 0.7961 (t0) REVERT: B 578 ASP cc_start: 0.8193 (t0) cc_final: 0.7935 (t0) REVERT: B 854 LYS cc_start: 0.7489 (tptt) cc_final: 0.7190 (tttp) REVERT: C 448 ASN cc_start: 0.8162 (t0) cc_final: 0.7619 (t0) REVERT: C 814 LYS cc_start: 0.8346 (mptt) cc_final: 0.7485 (mmmt) REVERT: C 935 GLN cc_start: 0.6364 (tt0) cc_final: 0.5879 (mt0) REVERT: C 1092 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8056 (mt-10) outliers start: 30 outliers final: 24 residues processed: 227 average time/residue: 0.3454 time to fit residues: 129.0609 Evaluate side-chains 231 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 275 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 217 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 339 HIS B 394 ASN C 207 HIS C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125728 restraints weight = 28320.848| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.88 r_work: 0.2961 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25520 Z= 0.130 Angle : 0.554 10.917 34812 Z= 0.272 Chirality : 0.046 0.357 4077 Planarity : 0.004 0.050 4404 Dihedral : 6.441 59.329 4326 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.34 % Allowed : 12.62 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.00 (0.15), residues: 3057 helix: 2.21 (0.21), residues: 666 sheet: 0.37 (0.21), residues: 627 loop : -1.06 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE B 92 TYR 0.023 0.001 TYR A 904 ARG 0.004 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 39) link_NAG-ASN : angle 2.68155 ( 117) link_BETA1-4 : bond 0.01028 ( 9) link_BETA1-4 : angle 2.66752 ( 27) hydrogen bonds : bond 0.04613 ( 916) hydrogen bonds : angle 4.80013 ( 2544) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.49674 ( 84) covalent geometry : bond 0.00312 (25428) covalent geometry : angle 0.52265 (34584) Misc. bond : bond 0.00467 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11507.99 seconds wall clock time: 198 minutes 14.08 seconds (11894.08 seconds total)