Starting phenix.real_space_refine on Mon Aug 25 03:59:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0v_42871/08_2025/8v0v_42871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0v_42871/08_2025/8v0v_42871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0v_42871/08_2025/8v0v_42871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0v_42871/08_2025/8v0v_42871.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0v_42871/08_2025/8v0v_42871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0v_42871/08_2025/8v0v_42871.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 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 15985 2.51 5 N 4115 2.21 5 O 4837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25051 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8159 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 52, 'TRANS': 991} Chain breaks: 6 Chain: "B" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8159 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 52, 'TRANS': 991} Chain breaks: 6 Chain: "A" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8159 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 52, 'TRANS': 991} Chain breaks: 6 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: "C" 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: 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 Chain: "A" 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: 4.87, per 1000 atoms: 0.19 Number of scatterers: 25051 At special positions: 0 Unit cell: (137.16, 131.76, 180.36, 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 4837 8.00 N 4115 7.00 C 15985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.04 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=2.02 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=2.05 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 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 50 sheets defined 25.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.049A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) 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: 3.638A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.025A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.391A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.612A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.554A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.556A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.622A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.806A 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 removed outlier: 3.965A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.506A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1150 removed outlier: 4.505A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.630A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.208A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.582A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.791A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.751A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.683A 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: 4.020A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.964A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.314A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.824A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.927A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.820A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (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 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.640A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.599A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.618A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.080A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.431A 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 1032 Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.544A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.007A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 104 removed outlier: 4.063A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.978A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.098A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.514A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.982A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.988A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.524A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.998A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.535A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.540A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.495A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.008A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.819A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.431A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.062A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.774A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.503A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.538A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.972A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.598A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AE1, first strand: chain 'A' and resid 25 through 30 removed outlier: 8.215A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.922A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.855A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AE5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.367A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AE7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.007A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AF5, first strand: chain 'A' and resid 1094 through 1097 929 hydrogen bonds defined for protein. 2562 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: 4.89 Time building geometry restraints manager: 2.19 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: 7972 1.35 - 1.47: 6614 1.47 - 1.60: 10885 1.60 - 1.73: 0 1.73 - 1.85: 141 Bond restraints: 25612 Sorted by residual: bond pdb=" C ALA A1056 " pdb=" N PRO A1057 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.90e+00 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.337 1.369 -0.032 1.24e-02 6.50e+03 6.77e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 25607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 34586 3.44 - 6.88: 221 6.88 - 10.32: 23 10.32 - 13.77: 6 13.77 - 17.21: 2 Bond angle restraints: 34838 Sorted by residual: angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 129.41 -15.01 2.30e+00 1.89e-01 4.26e+01 angle pdb=" CG1 ILE C 105 " pdb=" CB ILE C 105 " pdb=" CG2 ILE C 105 " ideal model delta sigma weight residual 110.70 93.49 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 127.31 -12.91 2.30e+00 1.89e-01 3.15e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 127.15 -12.75 2.30e+00 1.89e-01 3.07e+01 angle pdb=" N ASN C 122 " pdb=" CA ASN C 122 " pdb=" C ASN C 122 " ideal model delta sigma weight residual 112.59 106.41 6.18 1.22e+00 6.72e-01 2.56e+01 ... (remaining 34833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14145 18.05 - 36.11: 1383 36.11 - 54.16: 213 54.16 - 72.22: 58 72.22 - 90.27: 32 Dihedral angle restraints: 15831 sinusoidal: 6699 harmonic: 9132 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -13.99 -72.01 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 22.11 70.89 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -16.29 -69.71 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 15828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4040 0.154 - 0.308: 32 0.308 - 0.462: 4 0.462 - 0.616: 1 0.616 - 0.770: 1 Chirality restraints: 4078 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CB ILE B 101 " pdb=" CA ILE B 101 " pdb=" CG1 ILE B 101 " pdb=" CG2 ILE B 101 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 3.06 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 4075 not shown) Planarity restraints: 4486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 224 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO B 225 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 105 " 0.021 2.00e-02 2.50e+03 4.17e-02 1.73e+01 pdb=" C ILE C 105 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE C 105 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE C 106 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 126 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL A 126 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 126 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL A 127 " -0.022 2.00e-02 2.50e+03 ... (remaining 4483 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6588 2.81 - 3.33: 19978 3.33 - 3.85: 39864 3.85 - 4.38: 44794 4.38 - 4.90: 81296 Nonbonded interactions: 192520 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.331 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.336 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.344 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.347 3.040 ... (remaining 192515 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' and resid 24 through 1309) selection = (chain 'B' and resid 24 through 1309) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.230 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25694 Z= 0.228 Angle : 0.826 17.208 35043 Z= 0.428 Chirality : 0.056 0.770 4078 Planarity : 0.006 0.107 4451 Dihedral : 14.517 90.274 9828 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.13), residues: 3090 helix: -0.61 (0.17), residues: 688 sheet: 0.28 (0.19), residues: 654 loop : -1.79 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 237 TYR 0.038 0.002 TYR C 170 PHE 0.040 0.002 PHE B 906 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00486 (25612) covalent geometry : angle 0.80838 (34838) SS BOND : bond 0.00669 ( 41) SS BOND : angle 1.98535 ( 82) hydrogen bonds : bond 0.15123 ( 929) hydrogen bonds : angle 6.38273 ( 2562) link_BETA1-4 : bond 0.00863 ( 6) link_BETA1-4 : angle 1.88776 ( 18) link_NAG-ASN : bond 0.00567 ( 35) link_NAG-ASN : angle 2.70703 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 568 ASP cc_start: 0.7254 (t70) cc_final: 0.6944 (t0) REVERT: B 586 ASP cc_start: 0.8404 (m-30) cc_final: 0.8056 (m-30) REVERT: A 237 ARG cc_start: 0.7119 (mtp-110) cc_final: 0.6896 (mtp-110) REVERT: A 394 ASN cc_start: 0.6402 (m-40) cc_final: 0.6041 (m-40) REVERT: A 396 TYR cc_start: 0.8494 (m-80) cc_final: 0.8180 (m-10) REVERT: A 440 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8403 (ttmt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1687 time to fit residues: 64.1466 Evaluate side-chains 196 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0050 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.7980 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS B 30 ASN B 196 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 613 GLN B 675 GLN A 207 HIS A 339 HIS A 675 GLN A 901 GLN A 955 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123626 restraints weight = 28548.196| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.51 r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25694 Z= 0.096 Angle : 0.521 9.498 35043 Z= 0.268 Chirality : 0.043 0.235 4078 Planarity : 0.004 0.068 4451 Dihedral : 5.634 54.730 4212 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 0.40 % Allowed : 5.91 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.14), residues: 3090 helix: 1.10 (0.20), residues: 694 sheet: 0.53 (0.20), residues: 630 loop : -1.53 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.020 0.001 TYR C 170 PHE 0.026 0.001 PHE C 168 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00203 (25612) covalent geometry : angle 0.50525 (34838) SS BOND : bond 0.00255 ( 41) SS BOND : angle 1.63680 ( 82) hydrogen bonds : bond 0.04433 ( 929) hydrogen bonds : angle 4.82779 ( 2562) link_BETA1-4 : bond 0.00507 ( 6) link_BETA1-4 : angle 1.11956 ( 18) link_NAG-ASN : bond 0.00413 ( 35) link_NAG-ASN : angle 1.87165 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 549 THR cc_start: 0.8863 (m) cc_final: 0.8623 (t) REVERT: A 394 ASN cc_start: 0.6622 (m-40) cc_final: 0.6236 (m-40) REVERT: A 396 TYR cc_start: 0.8457 (m-80) cc_final: 0.8223 (m-10) REVERT: A 440 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8410 (ttmt) REVERT: A 606 ASN cc_start: 0.8569 (m-40) cc_final: 0.8280 (m-40) REVERT: A 1050 MET cc_start: 0.8647 (ptm) cc_final: 0.8376 (ptm) outliers start: 11 outliers final: 8 residues processed: 226 average time/residue: 0.1558 time to fit residues: 56.1888 Evaluate side-chains 208 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 241 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 255 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 296 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 207 HIS ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS A 339 HIS A 448 ASN A 675 GLN A 907 ASN A 955 ASN A1083 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.171348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123363 restraints weight = 28740.625| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.53 r_work: 0.3049 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25694 Z= 0.089 Angle : 0.489 8.619 35043 Z= 0.250 Chirality : 0.042 0.211 4078 Planarity : 0.003 0.059 4451 Dihedral : 5.017 53.820 4212 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 0.84 % Allowed : 7.89 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 3090 helix: 1.83 (0.20), residues: 679 sheet: 0.63 (0.20), residues: 654 loop : -1.42 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR A1067 PHE 0.028 0.001 PHE C 168 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00198 (25612) covalent geometry : angle 0.47445 (34838) SS BOND : bond 0.00243 ( 41) SS BOND : angle 1.56724 ( 82) hydrogen bonds : bond 0.03956 ( 929) hydrogen bonds : angle 4.40986 ( 2562) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 1.11705 ( 18) link_NAG-ASN : bond 0.00280 ( 35) link_NAG-ASN : angle 1.74573 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 529 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8243 (mmmt) REVERT: C 814 LYS cc_start: 0.7319 (mtpp) cc_final: 0.6971 (mmtp) REVERT: B 549 THR cc_start: 0.8877 (m) cc_final: 0.8669 (t) REVERT: A 394 ASN cc_start: 0.6700 (m-40) cc_final: 0.6366 (m-40) REVERT: A 396 TYR cc_start: 0.8500 (m-80) cc_final: 0.8212 (m-10) REVERT: A 606 ASN cc_start: 0.8553 (m-40) cc_final: 0.8269 (m-40) REVERT: A 1050 MET cc_start: 0.8728 (ptm) cc_final: 0.8454 (ptm) outliers start: 23 outliers final: 14 residues processed: 232 average time/residue: 0.1382 time to fit residues: 52.1831 Evaluate side-chains 217 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 115 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN B 30 ASN B 321 GLN B 675 GLN B1106 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113420 restraints weight = 28660.687| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.47 r_work: 0.2906 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 25694 Z= 0.258 Angle : 0.676 11.811 35043 Z= 0.346 Chirality : 0.048 0.316 4078 Planarity : 0.004 0.055 4451 Dihedral : 5.657 51.892 4212 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 1.73 % Allowed : 9.54 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3090 helix: 1.21 (0.20), residues: 715 sheet: 0.36 (0.20), residues: 649 loop : -1.59 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.023 0.002 TYR B 266 PHE 0.033 0.002 PHE B 906 TRP 0.011 0.002 TRP C 436 HIS 0.008 0.002 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00651 (25612) covalent geometry : angle 0.65247 (34838) SS BOND : bond 0.00459 ( 41) SS BOND : angle 2.74655 ( 82) hydrogen bonds : bond 0.06282 ( 929) hydrogen bonds : angle 4.80177 ( 2562) link_BETA1-4 : bond 0.00361 ( 6) link_BETA1-4 : angle 1.45574 ( 18) link_NAG-ASN : bond 0.00267 ( 35) link_NAG-ASN : angle 2.23355 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7094 (ttmm) cc_final: 0.6404 (pttt) REVERT: C 529 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8240 (mmmt) REVERT: C 814 LYS cc_start: 0.7424 (mtpp) cc_final: 0.6993 (mmtp) REVERT: B 237 ARG cc_start: 0.6998 (mtp-110) cc_final: 0.6767 (mtp-110) REVERT: B 960 ASN cc_start: 0.7866 (m-40) cc_final: 0.7480 (t0) REVERT: A 394 ASN cc_start: 0.7163 (m-40) cc_final: 0.6748 (m-40) REVERT: A 396 TYR cc_start: 0.8648 (m-80) cc_final: 0.8351 (m-10) REVERT: A 568 ASP cc_start: 0.6792 (t0) cc_final: 0.6465 (t0) REVERT: A 606 ASN cc_start: 0.8600 (m-40) cc_final: 0.8279 (m-40) outliers start: 47 outliers final: 34 residues processed: 253 average time/residue: 0.1623 time to fit residues: 65.9413 Evaluate side-chains 237 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 45 optimal weight: 1.9990 chunk 302 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 519 HIS C 804 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 675 GLN A 207 HIS A 245 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112700 restraints weight = 28725.108| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.49 r_work: 0.2891 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25694 Z= 0.213 Angle : 0.622 12.847 35043 Z= 0.317 Chirality : 0.046 0.328 4078 Planarity : 0.004 0.057 4451 Dihedral : 5.625 54.179 4212 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.31 % Allowed : 10.28 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3090 helix: 1.28 (0.20), residues: 715 sheet: 0.26 (0.20), residues: 653 loop : -1.57 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.020 0.001 TYR A1067 PHE 0.029 0.002 PHE C 168 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00531 (25612) covalent geometry : angle 0.59813 (34838) SS BOND : bond 0.00395 ( 41) SS BOND : angle 2.53828 ( 82) hydrogen bonds : bond 0.05650 ( 929) hydrogen bonds : angle 4.70048 ( 2562) link_BETA1-4 : bond 0.00311 ( 6) link_BETA1-4 : angle 1.43784 ( 18) link_NAG-ASN : bond 0.00435 ( 35) link_NAG-ASN : angle 2.19879 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7052 (ttmm) cc_final: 0.6404 (pttt) REVERT: C 420 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: C 529 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8182 (mmmt) REVERT: C 977 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 64 TRP cc_start: 0.6859 (t-100) cc_final: 0.6362 (t60) REVERT: B 237 ARG cc_start: 0.6899 (mtp-110) cc_final: 0.6652 (mtp-110) REVERT: B 568 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 960 ASN cc_start: 0.7877 (m-40) cc_final: 0.7496 (t0) REVERT: B 977 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 227 VAL cc_start: 0.6202 (OUTLIER) cc_final: 0.5988 (m) REVERT: A 394 ASN cc_start: 0.7136 (m-40) cc_final: 0.6742 (m-40) REVERT: A 396 TYR cc_start: 0.8646 (m-80) cc_final: 0.8351 (m-10) REVERT: A 460 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7299 (mtmm) REVERT: A 606 ASN cc_start: 0.8612 (m-40) cc_final: 0.8285 (m-40) outliers start: 63 outliers final: 43 residues processed: 261 average time/residue: 0.1687 time to fit residues: 70.4953 Evaluate side-chains 253 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 307 optimal weight: 0.7980 chunk 248 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN C 965 GLN B 405 ASN B 675 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114668 restraints weight = 28660.345| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.42 r_work: 0.2948 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25694 Z= 0.105 Angle : 0.535 10.011 35043 Z= 0.274 Chirality : 0.044 0.460 4078 Planarity : 0.004 0.056 4451 Dihedral : 5.238 54.896 4212 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 1.54 % Allowed : 11.67 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3090 helix: 1.78 (0.20), residues: 699 sheet: 0.38 (0.20), residues: 654 loop : -1.45 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.018 0.001 TYR B1067 PHE 0.030 0.001 PHE C 168 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00239 (25612) covalent geometry : angle 0.51198 (34838) SS BOND : bond 0.00279 ( 41) SS BOND : angle 2.26837 ( 82) hydrogen bonds : bond 0.04488 ( 929) hydrogen bonds : angle 4.47800 ( 2562) link_BETA1-4 : bond 0.00384 ( 6) link_BETA1-4 : angle 1.28112 ( 18) link_NAG-ASN : bond 0.00272 ( 35) link_NAG-ASN : angle 2.03566 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6222 (pttt) REVERT: C 529 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8128 (mmmt) REVERT: C 578 ASP cc_start: 0.8582 (t0) cc_final: 0.8202 (t0) REVERT: B 64 TRP cc_start: 0.6860 (t-100) cc_final: 0.6251 (t60) REVERT: B 237 ARG cc_start: 0.6824 (mtp-110) cc_final: 0.6566 (mtp-110) REVERT: B 902 MET cc_start: 0.8209 (mmt) cc_final: 0.7916 (mmm) REVERT: B 960 ASN cc_start: 0.7715 (m-40) cc_final: 0.7313 (t0) REVERT: B 977 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7615 (mp) REVERT: A 394 ASN cc_start: 0.6947 (m-40) cc_final: 0.6567 (m-40) REVERT: A 396 TYR cc_start: 0.8622 (m-80) cc_final: 0.8318 (m-10) REVERT: A 564 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7404 (mm-40) REVERT: A 606 ASN cc_start: 0.8596 (m-40) cc_final: 0.8313 (m-40) REVERT: A 646 ARG cc_start: 0.7972 (tpt-90) cc_final: 0.6827 (tpp80) outliers start: 42 outliers final: 27 residues processed: 248 average time/residue: 0.1476 time to fit residues: 59.0619 Evaluate side-chains 233 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 55 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 235 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN B 405 ASN B 675 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113972 restraints weight = 28590.610| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.45 r_work: 0.2941 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25694 Z= 0.118 Angle : 0.542 10.424 35043 Z= 0.275 Chirality : 0.044 0.406 4078 Planarity : 0.003 0.055 4451 Dihedral : 5.100 54.132 4212 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 1.80 % Allowed : 12.04 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 3090 helix: 2.02 (0.20), residues: 680 sheet: 0.31 (0.19), residues: 655 loop : -1.39 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.017 0.001 TYR A1067 PHE 0.028 0.001 PHE C 168 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00281 (25612) covalent geometry : angle 0.51952 (34838) SS BOND : bond 0.00285 ( 41) SS BOND : angle 2.36109 ( 82) hydrogen bonds : bond 0.04474 ( 929) hydrogen bonds : angle 4.44414 ( 2562) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.26422 ( 18) link_NAG-ASN : bond 0.00249 ( 35) link_NAG-ASN : angle 2.00957 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6117 (pttt) REVERT: C 578 ASP cc_start: 0.8582 (t0) cc_final: 0.8198 (t0) REVERT: C 977 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 64 TRP cc_start: 0.6895 (t-100) cc_final: 0.6289 (t60) REVERT: B 237 ARG cc_start: 0.6842 (mtp-110) cc_final: 0.6570 (mtp-110) REVERT: B 902 MET cc_start: 0.8289 (mmt) cc_final: 0.7931 (mmm) REVERT: B 960 ASN cc_start: 0.7685 (m-40) cc_final: 0.7278 (t0) REVERT: B 977 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7590 (mp) REVERT: A 394 ASN cc_start: 0.7042 (m-40) cc_final: 0.6599 (m-40) REVERT: A 460 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7106 (mtmm) REVERT: A 532 ASN cc_start: 0.8282 (t0) cc_final: 0.7999 (t0) REVERT: A 606 ASN cc_start: 0.8583 (m-40) cc_final: 0.8302 (m-40) REVERT: A 646 ARG cc_start: 0.7959 (tpt-90) cc_final: 0.6823 (tpp80) outliers start: 49 outliers final: 35 residues processed: 244 average time/residue: 0.1527 time to fit residues: 59.6175 Evaluate side-chains 237 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111236 restraints weight = 28707.174| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.44 r_work: 0.2876 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25694 Z= 0.251 Angle : 0.659 11.442 35043 Z= 0.335 Chirality : 0.048 0.428 4078 Planarity : 0.004 0.054 4451 Dihedral : 5.587 54.455 4212 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 2.09 % Allowed : 12.22 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3090 helix: 1.43 (0.20), residues: 709 sheet: 0.10 (0.19), residues: 654 loop : -1.50 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.022 0.002 TYR C 265 PHE 0.027 0.002 PHE C 168 TRP 0.010 0.002 TRP C 436 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00632 (25612) covalent geometry : angle 0.63412 (34838) SS BOND : bond 0.00454 ( 41) SS BOND : angle 2.79485 ( 82) hydrogen bonds : bond 0.05997 ( 929) hydrogen bonds : angle 4.75306 ( 2562) link_BETA1-4 : bond 0.00419 ( 6) link_BETA1-4 : angle 1.45308 ( 18) link_NAG-ASN : bond 0.00375 ( 35) link_NAG-ASN : angle 2.26853 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8162 (tm-30) REVERT: C 129 LYS cc_start: 0.7068 (ttmm) cc_final: 0.6451 (pttt) REVERT: C 417 ASN cc_start: 0.7509 (m-40) cc_final: 0.7204 (t0) REVERT: C 529 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8207 (mmmt) REVERT: C 578 ASP cc_start: 0.8660 (t0) cc_final: 0.8268 (t0) REVERT: C 690 GLN cc_start: 0.7256 (mm110) cc_final: 0.6840 (mm110) REVERT: C 977 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7643 (mp) REVERT: B 64 TRP cc_start: 0.6959 (t-100) cc_final: 0.6319 (t60) REVERT: B 237 ARG cc_start: 0.7038 (mtp-110) cc_final: 0.6735 (mtp-110) REVERT: B 578 ASP cc_start: 0.8729 (t0) cc_final: 0.8506 (t70) REVERT: B 960 ASN cc_start: 0.7918 (m-40) cc_final: 0.7537 (t0) REVERT: B 977 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7684 (mp) REVERT: A 394 ASN cc_start: 0.7090 (m-40) cc_final: 0.6704 (m-40) REVERT: A 460 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7155 (mtmm) REVERT: A 532 ASN cc_start: 0.8322 (t0) cc_final: 0.8072 (t0) REVERT: A 568 ASP cc_start: 0.7017 (t0) cc_final: 0.6584 (t0) REVERT: A 606 ASN cc_start: 0.8641 (m-40) cc_final: 0.8324 (m-40) outliers start: 57 outliers final: 46 residues processed: 248 average time/residue: 0.1670 time to fit residues: 66.2994 Evaluate side-chains 248 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 1.9990 chunk 242 optimal weight: 0.4980 chunk 289 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 207 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114918 restraints weight = 28691.303| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.48 r_work: 0.2947 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25694 Z= 0.120 Angle : 0.555 9.606 35043 Z= 0.282 Chirality : 0.044 0.446 4078 Planarity : 0.003 0.054 4451 Dihedral : 5.272 54.659 4212 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 1.76 % Allowed : 12.41 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3090 helix: 1.75 (0.20), residues: 707 sheet: 0.23 (0.19), residues: 653 loop : -1.40 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.017 0.001 TYR A1067 PHE 0.032 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00283 (25612) covalent geometry : angle 0.53206 (34838) SS BOND : bond 0.00305 ( 41) SS BOND : angle 2.38617 ( 82) hydrogen bonds : bond 0.04675 ( 929) hydrogen bonds : angle 4.52253 ( 2562) link_BETA1-4 : bond 0.00414 ( 6) link_BETA1-4 : angle 1.27523 ( 18) link_NAG-ASN : bond 0.00350 ( 35) link_NAG-ASN : angle 2.07030 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7002 (ttmm) cc_final: 0.6350 (pttt) REVERT: C 417 ASN cc_start: 0.7448 (m-40) cc_final: 0.7138 (t0) REVERT: C 578 ASP cc_start: 0.8632 (t0) cc_final: 0.8261 (t0) REVERT: C 690 GLN cc_start: 0.7176 (mm110) cc_final: 0.6819 (mm110) REVERT: C 935 GLN cc_start: 0.6809 (tt0) cc_final: 0.6519 (tt0) REVERT: B 64 TRP cc_start: 0.6874 (t-100) cc_final: 0.6294 (t60) REVERT: B 237 ARG cc_start: 0.6975 (mtp-110) cc_final: 0.6682 (mtp-110) REVERT: B 902 MET cc_start: 0.8258 (mmt) cc_final: 0.7966 (mmm) REVERT: B 960 ASN cc_start: 0.7780 (m-40) cc_final: 0.7394 (t0) REVERT: B 977 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7660 (mp) REVERT: A 394 ASN cc_start: 0.7127 (m-40) cc_final: 0.6712 (m-40) REVERT: A 452 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6738 (pt) REVERT: A 460 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7106 (mtmm) REVERT: A 532 ASN cc_start: 0.8303 (t0) cc_final: 0.8056 (t0) REVERT: A 606 ASN cc_start: 0.8597 (m-40) cc_final: 0.8288 (m-40) REVERT: A 646 ARG cc_start: 0.8043 (tpt-90) cc_final: 0.6854 (tpp80) outliers start: 48 outliers final: 40 residues processed: 233 average time/residue: 0.1604 time to fit residues: 59.6181 Evaluate side-chains 234 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 46 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN C1088 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109610 restraints weight = 28751.198| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.43 r_work: 0.2939 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25694 Z= 0.214 Angle : 0.627 10.880 35043 Z= 0.318 Chirality : 0.047 0.460 4078 Planarity : 0.004 0.052 4451 Dihedral : 5.491 52.781 4212 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 1.95 % Allowed : 12.41 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.14), residues: 3090 helix: 1.58 (0.20), residues: 707 sheet: 0.11 (0.19), residues: 654 loop : -1.47 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.019 0.002 TYR C 265 PHE 0.029 0.002 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00536 (25612) covalent geometry : angle 0.60175 (34838) SS BOND : bond 0.00400 ( 41) SS BOND : angle 2.70014 ( 82) hydrogen bonds : bond 0.05620 ( 929) hydrogen bonds : angle 4.67048 ( 2562) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 1.39362 ( 18) link_NAG-ASN : bond 0.00370 ( 35) link_NAG-ASN : angle 2.23281 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7091 (ttmm) cc_final: 0.6616 (pttt) REVERT: C 417 ASN cc_start: 0.7564 (m-40) cc_final: 0.7262 (t0) REVERT: C 529 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8175 (mmmt) REVERT: C 578 ASP cc_start: 0.8701 (t0) cc_final: 0.8330 (t0) REVERT: C 690 GLN cc_start: 0.7167 (mm110) cc_final: 0.6783 (mm110) REVERT: C 977 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 237 ARG cc_start: 0.7096 (mtp-110) cc_final: 0.6789 (mtp-110) REVERT: B 578 ASP cc_start: 0.8739 (t0) cc_final: 0.8519 (t70) REVERT: B 960 ASN cc_start: 0.7958 (m-40) cc_final: 0.7565 (t0) REVERT: B 977 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 394 ASN cc_start: 0.7220 (m-40) cc_final: 0.6790 (m-40) REVERT: A 452 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6837 (pt) REVERT: A 460 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7144 (mtmm) REVERT: A 568 ASP cc_start: 0.7098 (t0) cc_final: 0.6777 (t0) REVERT: A 606 ASN cc_start: 0.8712 (m-40) cc_final: 0.8448 (m-40) REVERT: A 646 ARG cc_start: 0.8086 (tpt-90) cc_final: 0.7001 (tpp80) outliers start: 53 outliers final: 44 residues processed: 231 average time/residue: 0.1681 time to fit residues: 62.0737 Evaluate side-chains 237 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 1 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS A 239 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111340 restraints weight = 28609.856| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.45 r_work: 0.2891 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25694 Z= 0.151 Angle : 0.576 9.986 35043 Z= 0.292 Chirality : 0.045 0.430 4078 Planarity : 0.004 0.053 4451 Dihedral : 5.339 54.101 4212 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 1.80 % Allowed : 12.59 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 3090 helix: 1.71 (0.20), residues: 705 sheet: 0.15 (0.19), residues: 656 loop : -1.42 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.018 0.001 TYR A1067 PHE 0.031 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00371 (25612) covalent geometry : angle 0.55180 (34838) SS BOND : bond 0.00339 ( 41) SS BOND : angle 2.48913 ( 82) hydrogen bonds : bond 0.04978 ( 929) hydrogen bonds : angle 4.55481 ( 2562) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 1.31830 ( 18) link_NAG-ASN : bond 0.00345 ( 35) link_NAG-ASN : angle 2.11323 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7246.77 seconds wall clock time: 124 minutes 26.43 seconds (7466.43 seconds total)