Starting phenix.real_space_refine on Sat May 24 02:26:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uir_42302/05_2025/8uir_42302.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uir_42302/05_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_42302/05_2025/8uir_42302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uir_42302/05_2025/8uir_42302.map" model { file = "/net/cci-nas-00/data/ceres_data/8uir_42302/05_2025/8uir_42302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uir_42302/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.75, per 1000 atoms: 0.59 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: 6.07 Conformation dependent library (CDL) restraints added in 3.6 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: 3.31 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: 10.53 Time building geometry restraints manager: 7.17 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: 1.380 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: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 56.360 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.310 ------------------------------------------------------------------------------- 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 : 2.479 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: 0.3376 time to fit residues: 122.7790 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 : 2.519 ------------------------------------------------------------------------------- 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 = 27374.896| |-----------------------------------------------------------------------------| 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: 0.7906 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 2.53976 ( 117) link_BETA1-4 : bond 0.00963 ( 9) link_BETA1-4 : angle 2.95577 ( 27) hydrogen bonds : bond 0.04780 ( 916) hydrogen bonds : angle 5.46817 ( 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 : 2.562 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7438 (t80) cc_final: 0.6890 (t80) REVERT: A 200 TYR cc_start: 0.5562 (t80) cc_final: 0.5163 (t80) REVERT: A 574 ASP cc_start: 0.8450 (t0) cc_final: 0.8215 (t0) REVERT: A 641 ASN cc_start: 0.7015 (m110) cc_final: 0.6675 (m110) REVERT: B 339 HIS cc_start: 0.7169 (t70) cc_final: 0.6939 (t70) REVERT: B 578 ASP cc_start: 0.7911 (t0) cc_final: 0.7641 (t0) REVERT: C 177 MET cc_start: 0.6238 (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: 0.7528 (t0) cc_final: 0.7133 (t0) REVERT: C 493 GLN cc_start: 0.7560 (tt0) cc_final: 0.7351 (tt0) outliers start: 12 outliers final: 8 residues processed: 224 average time/residue: 0.3434 time to fit residues: 125.1430 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 : 2.844 ------------------------------------------------------------------------------- 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: 2.9990 chunk 244 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 254 optimal weight: 0.0030 chunk 57 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 B 607 GLN B1010 GLN C 66 HIS C 405 ASN C 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117703 restraints weight = 27990.282| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.81 r_work: 0.2852 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25520 Z= 0.233 Angle : 0.652 10.580 34812 Z= 0.325 Chirality : 0.049 0.358 4077 Planarity : 0.004 0.056 4404 Dihedral : 7.131 59.832 4326 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.97 % Allowed : 7.94 % Favored : 91.09 % 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: -0.46 (0.15), residues: 3057 helix: 1.53 (0.21), residues: 651 sheet: 0.49 (0.21), residues: 606 loop : -1.36 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.007 0.001 HIS B1048 PHE 0.035 0.002 PHE B 906 TYR 0.016 0.002 TYR A 279 ARG 0.006 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 39) link_NAG-ASN : angle 2.80146 ( 117) link_BETA1-4 : bond 0.00941 ( 9) link_BETA1-4 : angle 3.02541 ( 27) hydrogen bonds : bond 0.06377 ( 916) hydrogen bonds : angle 5.33740 ( 2544) SS BOND : bond 0.00537 ( 42) SS BOND : angle 1.58933 ( 84) covalent geometry : bond 0.00578 (25428) covalent geometry : angle 0.62348 (34584) Misc. bond : bond 0.00056 ( 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 242 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7735 (t80) cc_final: 0.6993 (t80) REVERT: A 200 TYR cc_start: 0.5325 (t80) cc_final: 0.4913 (t80) REVERT: A 454 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7209 (ttm-80) REVERT: A 498 ARG cc_start: 0.6369 (mmt-90) cc_final: 0.5928 (mpt90) REVERT: A 641 ASN cc_start: 0.7069 (m110) cc_final: 0.6752 (m110) REVERT: A 751 ASN cc_start: 0.8580 (m-40) cc_final: 0.8332 (m-40) REVERT: B 48 LEU cc_start: 0.8552 (mm) cc_final: 0.8285 (mt) REVERT: B 339 HIS cc_start: 0.7254 (t70) cc_final: 0.6980 (t-90) REVERT: B 578 ASP cc_start: 0.8172 (t0) cc_final: 0.7879 (t0) REVERT: C 316 SER cc_start: 0.8966 (t) cc_final: 0.8736 (p) REVERT: C 388 ASN cc_start: 0.8992 (m-40) cc_final: 0.8740 (m-40) REVERT: C 448 ASN cc_start: 0.7835 (t0) cc_final: 0.7439 (t0) REVERT: C 814 LYS cc_start: 0.8468 (mptt) cc_final: 0.7630 (mmmt) REVERT: C 1092 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8046 (mt-10) outliers start: 26 outliers final: 19 residues processed: 230 average time/residue: 0.3372 time to fit residues: 126.1351 Evaluate side-chains 215 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 547 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 534 VAL 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 441 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 394 ASN B 901 GLN C 66 HIS C 314 GLN 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 = 0.3831 r_free = 0.3831 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119556 restraints weight = 27697.705| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.52 r_work: 0.3039 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1631 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= 0.119 Angle : 0.551 9.830 34812 Z= 0.270 Chirality : 0.045 0.403 4077 Planarity : 0.004 0.053 4404 Dihedral : 6.823 59.976 4326 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.78 % Allowed : 9.95 % Favored : 89.27 % 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: -0.31 (0.15), residues: 3057 helix: 1.78 (0.21), residues: 666 sheet: 0.51 (0.21), residues: 606 loop : -1.31 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.013 0.001 PHE B 377 TYR 0.014 0.001 TYR A1067 ARG 0.003 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 39) link_NAG-ASN : angle 2.67031 ( 117) link_BETA1-4 : bond 0.01033 ( 9) link_BETA1-4 : angle 2.87519 ( 27) hydrogen bonds : bond 0.04798 ( 916) hydrogen bonds : angle 5.03719 ( 2544) SS BOND : bond 0.00406 ( 42) SS BOND : angle 1.30405 ( 84) covalent geometry : bond 0.00276 (25428) covalent geometry : angle 0.52026 (34584) Misc. bond : bond 0.00025 ( 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 233 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7678 (t80) cc_final: 0.6963 (t80) REVERT: A 200 TYR cc_start: 0.5317 (t80) cc_final: 0.4878 (t80) REVERT: A 498 ARG cc_start: 0.6333 (mmt-90) cc_final: 0.5887 (mpt90) REVERT: A 574 ASP cc_start: 0.8523 (t0) cc_final: 0.8315 (t0) REVERT: A 641 ASN cc_start: 0.6959 (m110) cc_final: 0.6659 (m110) REVERT: A 751 ASN cc_start: 0.8523 (m-40) cc_final: 0.8283 (m-40) REVERT: B 339 HIS cc_start: 0.7150 (t70) cc_final: 0.6930 (t-90) REVERT: B 578 ASP cc_start: 0.8161 (t0) cc_final: 0.7875 (t0) REVERT: C 448 ASN cc_start: 0.7757 (t0) cc_final: 0.7381 (t0) REVERT: C 814 LYS cc_start: 0.8395 (mptt) cc_final: 0.7610 (mmtt) REVERT: C 1092 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7877 (mt-10) outliers start: 21 outliers final: 14 residues processed: 223 average time/residue: 0.3365 time to fit residues: 122.5330 Evaluate side-chains 214 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR 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 676 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 158 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 281 optimal weight: 0.0570 chunk 159 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 493 GLN B 394 ASN B1106 GLN C 207 HIS 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 = 0.3798 r_free = 0.3798 target = 0.164916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116139 restraints weight = 27724.186| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.53 r_work: 0.2884 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25520 Z= 0.193 Angle : 0.602 10.164 34812 Z= 0.297 Chirality : 0.047 0.366 4077 Planarity : 0.004 0.053 4404 Dihedral : 6.804 59.576 4326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.67 % Allowed : 10.02 % Favored : 88.31 % 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: -0.38 (0.15), residues: 3057 helix: 1.74 (0.21), residues: 663 sheet: 0.37 (0.21), residues: 606 loop : -1.32 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS B1048 PHE 0.020 0.002 PHE B 168 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 39) link_NAG-ASN : angle 2.70741 ( 117) link_BETA1-4 : bond 0.00987 ( 9) link_BETA1-4 : angle 2.86009 ( 27) hydrogen bonds : bond 0.05628 ( 916) hydrogen bonds : angle 5.08941 ( 2544) SS BOND : bond 0.00515 ( 42) SS BOND : angle 1.59532 ( 84) covalent geometry : bond 0.00480 (25428) covalent geometry : angle 0.57179 (34584) Misc. bond : bond 0.00185 ( 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 250 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 2.674 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.7012 (tpp-160) REVERT: A 170 TYR cc_start: 0.7662 (t80) cc_final: 0.6919 (t80) REVERT: A 392 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: A 498 ARG cc_start: 0.6062 (mmt-90) cc_final: 0.5658 (mpt90) REVERT: A 568 ASP cc_start: 0.7269 (t0) cc_final: 0.7053 (t0) REVERT: A 641 ASN cc_start: 0.6960 (m110) cc_final: 0.6672 (m110) REVERT: B 200 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.4262 (m-80) REVERT: B 339 HIS cc_start: 0.7297 (t70) cc_final: 0.7015 (t-90) REVERT: B 578 ASP cc_start: 0.8243 (t0) cc_final: 0.7934 (t0) REVERT: B 854 LYS cc_start: 0.7703 (tptt) cc_final: 0.7398 (tttp) REVERT: C 66 HIS cc_start: 0.7010 (m-70) cc_final: 0.6797 (m-70) REVERT: C 316 SER cc_start: 0.8927 (t) cc_final: 0.8664 (p) REVERT: C 448 ASN cc_start: 0.7961 (t0) cc_final: 0.7454 (t0) REVERT: C 814 LYS cc_start: 0.8454 (mptt) cc_final: 0.7523 (mttm) REVERT: C 1092 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8061 (mt-10) outliers start: 45 outliers final: 28 residues processed: 237 average time/residue: 0.3362 time to fit residues: 129.6748 Evaluate side-chains 226 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 2.664 ------------------------------------------------------------------------------- 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 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 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 1050 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 534 VAL 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 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL 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 676 THR 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: 0.9980 chunk 153 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 232 optimal weight: 0.0980 chunk 194 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 394 ASN C 207 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 = 0.3828 r_free = 0.3828 target = 0.167702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124207 restraints weight = 27460.283| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.17 r_work: 0.2919 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25520 Z= 0.113 Angle : 0.536 10.381 34812 Z= 0.264 Chirality : 0.045 0.341 4077 Planarity : 0.003 0.052 4404 Dihedral : 6.555 58.797 4326 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.22 % Allowed : 11.43 % Favored : 87.34 % 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: -0.11 (0.15), residues: 3057 helix: 2.15 (0.21), residues: 648 sheet: 0.48 (0.21), residues: 600 loop : -1.17 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.014 0.001 PHE C 592 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 39) link_NAG-ASN : angle 2.58738 ( 117) link_BETA1-4 : bond 0.00997 ( 9) link_BETA1-4 : angle 2.80029 ( 27) hydrogen bonds : bond 0.04525 ( 916) hydrogen bonds : angle 4.88644 ( 2544) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.34943 ( 84) covalent geometry : bond 0.00263 (25428) covalent geometry : angle 0.50604 (34584) Misc. bond : bond 0.00103 ( 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 235 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7650 (t80) cc_final: 0.6869 (t80) REVERT: A 200 TYR cc_start: 0.5059 (t80) cc_final: 0.4415 (t80) REVERT: A 392 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: A 498 ARG cc_start: 0.6043 (mmt-90) cc_final: 0.5547 (mpt90) REVERT: A 641 ASN cc_start: 0.6955 (m110) cc_final: 0.6658 (m110) REVERT: B 200 TYR cc_start: 0.5438 (OUTLIER) cc_final: 0.4312 (m-80) REVERT: B 339 HIS cc_start: 0.7308 (t70) cc_final: 0.7013 (t-90) REVERT: B 568 ASP cc_start: 0.7755 (t0) cc_final: 0.7290 (t0) REVERT: B 574 ASP cc_start: 0.8341 (t0) cc_final: 0.7782 (t0) REVERT: B 578 ASP cc_start: 0.8227 (t0) cc_final: 0.7921 (t0) REVERT: B 854 LYS cc_start: 0.7513 (tptt) cc_final: 0.7226 (tptt) REVERT: C 66 HIS cc_start: 0.6917 (m-70) cc_final: 0.6684 (m-70) REVERT: C 316 SER cc_start: 0.8925 (t) cc_final: 0.8675 (p) REVERT: C 368 ILE cc_start: 0.8455 (mt) cc_final: 0.8170 (mm) REVERT: C 448 ASN cc_start: 0.8025 (t0) cc_final: 0.7512 (t0) REVERT: C 814 LYS cc_start: 0.8399 (mptt) cc_final: 0.7521 (mmmt) REVERT: C 1092 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7998 (mt-10) outliers start: 33 outliers final: 21 residues processed: 225 average time/residue: 0.3373 time to fit residues: 125.9424 Evaluate side-chains 216 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 2.851 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain A residue 465 GLU 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 B residue 52 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN 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 645 THR Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 239 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 141 optimal weight: 0.0040 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 overall best weight: 1.5894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN C 314 GLN C 339 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.165159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122523 restraints weight = 27644.698| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.22 r_work: 0.2885 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25520 Z= 0.175 Angle : 0.578 10.893 34812 Z= 0.285 Chirality : 0.047 0.379 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.612 59.029 4326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.52 % Allowed : 11.73 % Favored : 86.75 % 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: -0.18 (0.15), residues: 3057 helix: 2.08 (0.21), residues: 645 sheet: 0.31 (0.21), residues: 624 loop : -1.17 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.001 PHE B 168 TYR 0.016 0.001 TYR A1067 ARG 0.002 0.000 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 39) link_NAG-ASN : angle 2.65052 ( 117) link_BETA1-4 : bond 0.01047 ( 9) link_BETA1-4 : angle 2.80048 ( 27) hydrogen bonds : bond 0.05252 ( 916) hydrogen bonds : angle 4.94218 ( 2544) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.52627 ( 84) covalent geometry : bond 0.00433 (25428) covalent geometry : angle 0.54814 (34584) Misc. bond : bond 0.00102 ( 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 243 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7253 (tpp-160) REVERT: A 170 TYR cc_start: 0.7689 (t80) cc_final: 0.6886 (t80) REVERT: A 392 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: A 498 ARG cc_start: 0.6167 (mmt-90) cc_final: 0.5646 (mpt90) REVERT: A 568 ASP cc_start: 0.7245 (t0) cc_final: 0.7043 (t0) REVERT: A 641 ASN cc_start: 0.6962 (m110) cc_final: 0.6666 (m110) REVERT: B 200 TYR cc_start: 0.5401 (OUTLIER) cc_final: 0.3942 (m-80) REVERT: B 339 HIS cc_start: 0.7326 (t70) cc_final: 0.7025 (t-90) REVERT: B 377 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6268 (t80) REVERT: B 574 ASP cc_start: 0.8422 (t0) cc_final: 0.8109 (t0) REVERT: B 578 ASP cc_start: 0.8279 (t0) cc_final: 0.7955 (t0) REVERT: B 854 LYS cc_start: 0.7514 (tptt) cc_final: 0.7210 (tttp) REVERT: C 66 HIS cc_start: 0.7033 (m-70) cc_final: 0.6783 (m-70) REVERT: C 314 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8173 (mm-40) REVERT: C 316 SER cc_start: 0.8983 (t) cc_final: 0.8732 (p) REVERT: C 368 ILE cc_start: 0.8516 (mt) cc_final: 0.8221 (mm) REVERT: C 448 ASN cc_start: 0.8050 (t0) cc_final: 0.7457 (t0) REVERT: C 814 LYS cc_start: 0.8419 (mptt) cc_final: 0.7513 (mmmt) REVERT: C 1092 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8022 (mt-10) outliers start: 41 outliers final: 28 residues processed: 231 average time/residue: 0.3372 time to fit residues: 128.0822 Evaluate side-chains 229 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 368 ILE 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 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 1050 MET Chi-restraints excluded: chain B residue 52 GLN 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 1081 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 266 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 394 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 314 GLN C 339 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125167 restraints weight = 28254.725| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.42 r_work: 0.2979 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25520 Z= 0.228 Angle : 0.656 22.302 34812 Z= 0.321 Chirality : 0.049 0.581 4077 Planarity : 0.004 0.053 4404 Dihedral : 6.860 59.946 4326 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.60 % Allowed : 11.92 % Favored : 86.49 % 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: -0.36 (0.15), residues: 3057 helix: 1.93 (0.21), residues: 642 sheet: 0.30 (0.21), residues: 603 loop : -1.30 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 886 HIS 0.007 0.001 HIS B1048 PHE 0.022 0.002 PHE C 377 TYR 0.024 0.002 TYR C 313 ARG 0.003 0.000 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 39) link_NAG-ASN : angle 3.66706 ( 117) link_BETA1-4 : bond 0.00986 ( 9) link_BETA1-4 : angle 2.80795 ( 27) hydrogen bonds : bond 0.06008 ( 916) hydrogen bonds : angle 5.10725 ( 2544) SS BOND : bond 0.00538 ( 42) SS BOND : angle 1.67358 ( 84) covalent geometry : bond 0.00572 (25428) covalent geometry : angle 0.61266 (34584) Misc. bond : bond 0.00120 ( 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 241 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7438 (tpp-160) REVERT: A 170 TYR cc_start: 0.7803 (t80) cc_final: 0.7042 (t80) REVERT: A 392 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: A 498 ARG cc_start: 0.6518 (mmt-90) cc_final: 0.6283 (mmt180) REVERT: A 568 ASP cc_start: 0.7290 (t0) cc_final: 0.7075 (t0) REVERT: A 641 ASN cc_start: 0.6920 (m110) cc_final: 0.6673 (m110) REVERT: B 377 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6418 (t80) REVERT: B 578 ASP cc_start: 0.8307 (t0) cc_final: 0.8059 (t0) REVERT: B 854 LYS cc_start: 0.7591 (tptt) cc_final: 0.7357 (tttp) REVERT: C 66 HIS cc_start: 0.7216 (m-70) cc_final: 0.6955 (m-70) REVERT: C 177 MET cc_start: 0.5387 (pmm) cc_final: 0.4582 (ptp) REVERT: C 316 SER cc_start: 0.8971 (t) cc_final: 0.8766 (p) REVERT: C 448 ASN cc_start: 0.8182 (t0) cc_final: 0.7574 (t0) REVERT: C 814 LYS cc_start: 0.8472 (mptt) cc_final: 0.7546 (mtpp) REVERT: C 1092 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8147 (mt-10) outliers start: 43 outliers final: 33 residues processed: 231 average time/residue: 0.3403 time to fit residues: 129.6124 Evaluate side-chains 229 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 2.581 ------------------------------------------------------------------------------- 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 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 1050 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 383 SER 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 878 LEU 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 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 745 ASP 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: 4.9990 chunk 214 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 299 optimal weight: 0.5980 chunk 304 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 292 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 394 ASN C 207 HIS C 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.168090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125787 restraints weight = 28387.514| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.83 r_work: 0.2964 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2145 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= 0.119 Angle : 0.553 11.572 34812 Z= 0.271 Chirality : 0.045 0.360 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.582 58.998 4326 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -0.13 (0.15), residues: 3057 helix: 2.20 (0.21), residues: 648 sheet: 0.43 (0.21), residues: 573 loop : -1.17 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C 66 PHE 0.021 0.001 PHE B 168 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 39) link_NAG-ASN : angle 2.94809 ( 117) link_BETA1-4 : bond 0.00986 ( 9) link_BETA1-4 : angle 2.73682 ( 27) hydrogen bonds : bond 0.04597 ( 916) hydrogen bonds : angle 4.88331 ( 2544) SS BOND : bond 0.00400 ( 42) SS BOND : angle 1.34341 ( 84) covalent geometry : bond 0.00279 (25428) covalent geometry : angle 0.51734 (34584) Misc. bond : bond 0.00084 ( 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 237 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7538 (tpp-160) cc_final: 0.7207 (tpp-160) REVERT: A 170 TYR cc_start: 0.7676 (t80) cc_final: 0.6712 (t80) REVERT: A 200 TYR cc_start: 0.4986 (t80) cc_final: 0.4347 (t80) REVERT: A 392 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: A 498 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.6239 (mpt90) REVERT: A 568 ASP cc_start: 0.7312 (t0) cc_final: 0.7061 (t0) REVERT: A 641 ASN cc_start: 0.6960 (m110) cc_final: 0.6704 (m110) REVERT: B 377 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6181 (t80) REVERT: B 568 ASP cc_start: 0.7819 (t0) cc_final: 0.7401 (t0) REVERT: B 574 ASP cc_start: 0.8481 (t0) cc_final: 0.7999 (t0) REVERT: B 578 ASP cc_start: 0.8263 (t0) cc_final: 0.8010 (t0) REVERT: B 854 LYS cc_start: 0.7523 (tptt) cc_final: 0.7244 (tttp) REVERT: C 66 HIS cc_start: 0.6920 (m-70) cc_final: 0.6667 (m-70) REVERT: C 177 MET cc_start: 0.5355 (pmm) cc_final: 0.4859 (pmm) REVERT: C 207 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7513 (m90) REVERT: C 448 ASN cc_start: 0.8211 (t0) cc_final: 0.7641 (t0) REVERT: C 814 LYS cc_start: 0.8363 (mptt) cc_final: 0.7479 (mmmt) REVERT: C 1092 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8249 (mt-10) outliers start: 40 outliers final: 29 residues processed: 224 average time/residue: 0.3289 time to fit residues: 121.0440 Evaluate side-chains 229 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 2.801 ------------------------------------------------------------------------------- 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 302 THR 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 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 1050 MET Chi-restraints excluded: chain B residue 52 GLN 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 723 THR 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 207 HIS 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 900 MET 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: 2.9990 chunk 58 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 178 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3845 r_free = 0.3845 target = 0.167914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125519 restraints weight = 28304.116| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.91 r_work: 0.2980 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 0.040 25520 Z= 0.127 Angle : 0.563 12.741 34812 Z= 0.275 Chirality : 0.046 0.362 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.555 59.126 4326 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.30 % Allowed : 12.58 % 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: -0.09 (0.15), residues: 3057 helix: 2.24 (0.21), residues: 648 sheet: 0.45 (0.21), residues: 573 loop : -1.15 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.007 0.001 HIS C 207 PHE 0.019 0.001 PHE B 92 TYR 0.017 0.001 TYR A 904 ARG 0.002 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 39) link_NAG-ASN : angle 3.10906 ( 117) link_BETA1-4 : bond 0.01001 ( 9) link_BETA1-4 : angle 2.72902 ( 27) hydrogen bonds : bond 0.04671 ( 916) hydrogen bonds : angle 4.85728 ( 2544) SS BOND : bond 0.00403 ( 42) SS BOND : angle 1.33327 ( 84) covalent geometry : bond 0.00303 (25428) covalent geometry : angle 0.52607 (34584) Misc. bond : bond 0.00081 ( 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 231 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7606 (tpp-160) cc_final: 0.7284 (tpp-160) REVERT: A 170 TYR cc_start: 0.7737 (t80) cc_final: 0.6855 (t80) REVERT: A 200 TYR cc_start: 0.5007 (t80) cc_final: 0.4344 (t80) REVERT: A 392 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: A 498 ARG cc_start: 0.6450 (mmt-90) cc_final: 0.6176 (mpt90) REVERT: A 568 ASP cc_start: 0.7236 (t0) cc_final: 0.6988 (t0) REVERT: A 641 ASN cc_start: 0.6979 (m110) cc_final: 0.6726 (m110) REVERT: A 916 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 377 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6251 (t80) REVERT: B 568 ASP cc_start: 0.7809 (t0) cc_final: 0.7406 (t0) REVERT: B 574 ASP cc_start: 0.8493 (t0) cc_final: 0.8019 (t0) REVERT: B 578 ASP cc_start: 0.8258 (t0) cc_final: 0.8003 (t0) REVERT: B 854 LYS cc_start: 0.7546 (tptt) cc_final: 0.7249 (tttp) REVERT: C 66 HIS cc_start: 0.6963 (m-70) cc_final: 0.6691 (m-70) REVERT: C 177 MET cc_start: 0.5353 (pmm) cc_final: 0.4974 (pmm) REVERT: C 448 ASN cc_start: 0.8227 (t0) cc_final: 0.7599 (t0) REVERT: C 814 LYS cc_start: 0.8385 (mptt) cc_final: 0.7474 (mmmt) outliers start: 35 outliers final: 28 residues processed: 220 average time/residue: 0.3570 time to fit residues: 127.7609 Evaluate side-chains 227 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 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 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 1050 MET Chi-restraints excluded: chain B residue 52 GLN 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 723 THR 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 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 900 MET 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: 0.9980 chunk 155 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 207 HIS C 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124172 restraints weight = 28369.828| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.79 r_work: 0.2922 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25520 Z= 0.154 Angle : 0.581 12.172 34812 Z= 0.286 Chirality : 0.047 0.360 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.579 59.643 4326 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.34 % Allowed : 12.77 % Favored : 85.89 % 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: -0.12 (0.15), residues: 3057 helix: 2.19 (0.21), residues: 645 sheet: 0.32 (0.21), residues: 597 loop : -1.12 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.005 0.001 HIS B1048 PHE 0.023 0.001 PHE B 168 TYR 0.016 0.001 TYR A1067 ARG 0.002 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 39) link_NAG-ASN : angle 2.78597 ( 117) link_BETA1-4 : bond 0.00976 ( 9) link_BETA1-4 : angle 2.69872 ( 27) hydrogen bonds : bond 0.05135 ( 916) hydrogen bonds : angle 4.90995 ( 2544) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.45702 ( 84) covalent geometry : bond 0.00377 (25428) covalent geometry : angle 0.55053 (34584) Misc. bond : bond 0.00089 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10986.46 seconds wall clock time: 191 minutes 18.77 seconds (11478.77 seconds total)