Starting phenix.real_space_refine on Sat May 24 05:45:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0v_42871/05_2025/8v0v_42871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0v_42871/05_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_42871/05_2025/8v0v_42871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0v_42871/05_2025/8v0v_42871.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0v_42871/05_2025/8v0v_42871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0v_42871/05_2025/8v0v_42871.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.93, per 1000 atoms: 0.56 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: 5.85 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.59 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: 10.13 Time building geometry restraints manager: 7.00 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 1150 or resid 1301 through 1309)) selection = (chain 'B' and (resid 24 through 1150 or resid 1301 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.080 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (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 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS C 207 PHE 0.040 0.002 PHE B 906 TYR 0.038 0.002 TYR C 170 ARG 0.011 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 35) link_NAG-ASN : angle 2.70703 ( 105) link_BETA1-4 : bond 0.00863 ( 6) link_BETA1-4 : angle 1.88776 ( 18) hydrogen bonds : bond 0.15123 ( 929) hydrogen bonds : angle 6.38273 ( 2562) SS BOND : bond 0.00669 ( 41) SS BOND : angle 1.98535 ( 82) covalent geometry : bond 0.00486 (25612) covalent geometry : angle 0.80838 (34838) *********************** 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 : 2.515 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: 0.6030 (m-40) REVERT: A 396 TYR cc_start: 0.8494 (m-80) cc_final: 0.8190 (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: 0.3554 time to fit residues: 134.9949 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 : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN 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 = 0.3871 r_free = 0.3871 target = 0.167141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119105 restraints weight = 28422.317| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.44 r_work: 0.3003 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25694 Z= 0.111 Angle : 0.539 9.534 35043 Z= 0.278 Chirality : 0.043 0.238 4078 Planarity : 0.004 0.069 4451 Dihedral : 5.755 53.855 4212 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 0.66 % Allowed : 5.76 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3090 helix: 0.90 (0.20), residues: 704 sheet: 0.46 (0.20), residues: 642 loop : -1.58 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 PHE 0.025 0.001 PHE C 168 TYR 0.020 0.001 TYR C 170 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 35) link_NAG-ASN : angle 1.94354 ( 105) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 1.18850 ( 18) hydrogen bonds : bond 0.04766 ( 929) hydrogen bonds : angle 4.87285 ( 2562) SS BOND : bond 0.00290 ( 41) SS BOND : angle 1.76841 ( 82) covalent geometry : bond 0.00251 (25612) covalent geometry : angle 0.52182 (34838) *********************** 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 232 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.6672 (m-40) cc_final: 0.6229 (m-40) REVERT: A 440 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8409 (ttmt) REVERT: A 923 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 1050 MET cc_start: 0.8691 (ptm) cc_final: 0.8441 (ptm) outliers start: 18 outliers final: 14 residues processed: 225 average time/residue: 0.3518 time to fit residues: 126.9991 Evaluate side-chains 214 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 833 PHE 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 752 LEU Chi-restraints excluded: chain A residue 923 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 280 optimal weight: 0.3980 chunk 52 optimal weight: 0.0030 chunk 233 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- 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 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1106 GLN A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 675 GLN A 907 ASN A 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115779 restraints weight = 28370.274| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.52 r_work: 0.2945 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25694 Z= 0.178 Angle : 0.594 9.863 35043 Z= 0.304 Chirality : 0.045 0.280 4078 Planarity : 0.004 0.059 4451 Dihedral : 5.545 53.029 4212 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 1.28 % Allowed : 8.08 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3090 helix: 1.33 (0.20), residues: 693 sheet: 0.42 (0.20), residues: 655 loop : -1.59 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS A1083 PHE 0.024 0.002 PHE C 168 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 35) link_NAG-ASN : angle 2.04834 ( 105) link_BETA1-4 : bond 0.00340 ( 6) link_BETA1-4 : angle 1.32383 ( 18) hydrogen bonds : bond 0.05395 ( 929) hydrogen bonds : angle 4.70500 ( 2562) SS BOND : bond 0.00358 ( 41) SS BOND : angle 2.31090 ( 82) covalent geometry : bond 0.00440 (25612) covalent geometry : angle 0.57336 (34838) *********************** 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 240 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7139 (ttmm) cc_final: 0.6315 (pttt) REVERT: C 170 TYR cc_start: 0.7387 (t80) cc_final: 0.7127 (t80) REVERT: C 529 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8232 (mmmt) REVERT: C 814 LYS cc_start: 0.7535 (mtpp) cc_final: 0.7067 (mmtp) REVERT: B 390 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7200 (pp) REVERT: B 501 TYR cc_start: 0.7478 (m-10) cc_final: 0.7140 (m-10) REVERT: A 394 ASN cc_start: 0.6932 (m-40) cc_final: 0.6526 (m-40) REVERT: A 440 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8401 (ttmt) REVERT: A 923 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 1050 MET cc_start: 0.8897 (ptm) cc_final: 0.8673 (ptm) outliers start: 35 outliers final: 25 residues processed: 230 average time/residue: 0.3575 time to fit residues: 131.8159 Evaluate side-chains 228 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 ILE Chi-restraints excluded: chain C residue 524 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 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 923 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 188 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 C 804 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117548 restraints weight = 28724.073| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.49 r_work: 0.2971 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25694 Z= 0.120 Angle : 0.554 16.600 35043 Z= 0.279 Chirality : 0.044 0.364 4078 Planarity : 0.004 0.056 4451 Dihedral : 5.399 54.223 4212 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 1.32 % Allowed : 9.65 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3090 helix: 1.67 (0.20), residues: 689 sheet: 0.45 (0.20), residues: 645 loop : -1.51 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A1083 PHE 0.029 0.001 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.007 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 35) link_NAG-ASN : angle 2.68124 ( 105) link_BETA1-4 : bond 0.00369 ( 6) link_BETA1-4 : angle 1.22205 ( 18) hydrogen bonds : bond 0.04626 ( 929) hydrogen bonds : angle 4.54056 ( 2562) SS BOND : bond 0.00284 ( 41) SS BOND : angle 2.20356 ( 82) covalent geometry : bond 0.00282 (25612) covalent geometry : angle 0.52453 (34838) *********************** 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 239 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7034 (ttmm) cc_final: 0.6329 (pttt) REVERT: C 170 TYR cc_start: 0.7508 (t80) cc_final: 0.7181 (t80) REVERT: C 529 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8263 (mmmt) REVERT: B 237 ARG cc_start: 0.6763 (mtp-110) cc_final: 0.6511 (mtp-110) REVERT: B 390 LEU cc_start: 0.7521 (pp) cc_final: 0.7282 (pp) REVERT: B 501 TYR cc_start: 0.7522 (m-10) cc_final: 0.7208 (m-10) REVERT: B 955 ASN cc_start: 0.7634 (m-40) cc_final: 0.7286 (m110) REVERT: A 394 ASN cc_start: 0.6967 (m-40) cc_final: 0.6554 (m-40) REVERT: A 460 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7236 (mtmm) REVERT: A 1050 MET cc_start: 0.8903 (ptm) cc_final: 0.8701 (ptm) outliers start: 36 outliers final: 26 residues processed: 231 average time/residue: 0.3556 time to fit residues: 131.2877 Evaluate side-chains 229 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 2.530 ------------------------------------------------------------------------------- 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 375 PHE 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 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 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 947 LYS 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 424 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 649 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 168 optimal weight: 0.0010 chunk 15 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 2 optimal weight: 0.0470 chunk 269 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 overall best weight: 0.5284 ------------------------------------------------------------------------------- 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 C 804 GLN C 965 GLN C1106 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116767 restraints weight = 28412.106| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.48 r_work: 0.3020 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1379 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= 0.094 Angle : 0.508 13.856 35043 Z= 0.258 Chirality : 0.043 0.211 4078 Planarity : 0.003 0.056 4451 Dihedral : 4.972 54.401 4212 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 10.17 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3090 helix: 1.86 (0.20), residues: 701 sheet: 0.55 (0.20), residues: 648 loop : -1.39 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.003 0.000 HIS A1083 PHE 0.027 0.001 PHE C 168 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 35) link_NAG-ASN : angle 2.19184 ( 105) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 1.16779 ( 18) hydrogen bonds : bond 0.04056 ( 929) hydrogen bonds : angle 4.34361 ( 2562) SS BOND : bond 0.00245 ( 41) SS BOND : angle 2.00553 ( 82) covalent geometry : bond 0.00210 (25612) covalent geometry : angle 0.48470 (34838) *********************** 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 261 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7037 (ttmm) cc_final: 0.6344 (pttt) REVERT: C 170 TYR cc_start: 0.7486 (t80) cc_final: 0.6998 (t80) REVERT: C 171 VAL cc_start: 0.8466 (t) cc_final: 0.8007 (m) REVERT: C 420 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: C 529 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8158 (mmmt) REVERT: B 501 TYR cc_start: 0.7682 (m-10) cc_final: 0.7326 (m-10) REVERT: B 960 ASN cc_start: 0.7742 (m-40) cc_final: 0.7374 (t0) REVERT: A 394 ASN cc_start: 0.6922 (m-40) cc_final: 0.6465 (m-40) REVERT: A 460 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7245 (mtmm) REVERT: A 564 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7473 (mm-40) REVERT: A 1050 MET cc_start: 0.8895 (ptm) cc_final: 0.8686 (ptm) outliers start: 44 outliers final: 26 residues processed: 250 average time/residue: 0.3638 time to fit residues: 147.8459 Evaluate side-chains 230 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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 375 PHE 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 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 291 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1133 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 136 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 186 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 C 804 GLN B 675 GLN A 207 HIS A 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.168001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117318 restraints weight = 28389.051| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.47 r_work: 0.3008 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25694 Z= 0.093 Angle : 0.505 11.842 35043 Z= 0.256 Chirality : 0.043 0.235 4078 Planarity : 0.003 0.056 4451 Dihedral : 4.787 54.074 4212 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 1.47 % Allowed : 10.83 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3090 helix: 1.96 (0.20), residues: 701 sheet: 0.58 (0.20), residues: 636 loop : -1.31 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.002 0.000 HIS A1083 PHE 0.014 0.001 PHE C 374 TYR 0.018 0.001 TYR B1067 ARG 0.009 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 35) link_NAG-ASN : angle 2.00812 ( 105) link_BETA1-4 : bond 0.00420 ( 6) link_BETA1-4 : angle 1.15055 ( 18) hydrogen bonds : bond 0.03962 ( 929) hydrogen bonds : angle 4.30573 ( 2562) SS BOND : bond 0.00237 ( 41) SS BOND : angle 2.05971 ( 82) covalent geometry : bond 0.00210 (25612) covalent geometry : angle 0.48299 (34838) *********************** 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 245 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 2.567 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: 0.7112 (ttmm) cc_final: 0.6407 (pttt) REVERT: C 170 TYR cc_start: 0.7594 (t80) cc_final: 0.7203 (t80) REVERT: B 237 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.6673 (mtp-110) REVERT: B 501 TYR cc_start: 0.7785 (m-10) cc_final: 0.7433 (m-10) REVERT: B 960 ASN cc_start: 0.7841 (m-40) cc_final: 0.7482 (t0) REVERT: A 394 ASN cc_start: 0.6933 (m-40) cc_final: 0.6494 (m-40) REVERT: A 460 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7272 (mtmm) REVERT: A 564 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7501 (mm-40) REVERT: A 1050 MET cc_start: 0.8978 (ptm) cc_final: 0.8773 (ptm) outliers start: 40 outliers final: 32 residues processed: 235 average time/residue: 0.3559 time to fit residues: 133.4944 Evaluate side-chains 230 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 375 PHE 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 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 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL 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 460 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 20.0000 chunk 273 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 282 optimal weight: 0.0040 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 C1088 HIS B 544 ASN B 675 GLN A 207 HIS A 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116122 restraints weight = 28524.327| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.50 r_work: 0.2954 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25694 Z= 0.149 Angle : 0.556 10.991 35043 Z= 0.283 Chirality : 0.044 0.222 4078 Planarity : 0.004 0.054 4451 Dihedral : 4.980 53.251 4212 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 1.73 % Allowed : 11.23 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3090 helix: 1.92 (0.20), residues: 691 sheet: 0.43 (0.20), residues: 643 loop : -1.36 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS A1058 PHE 0.025 0.001 PHE C 168 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 35) link_NAG-ASN : angle 2.07066 ( 105) link_BETA1-4 : bond 0.00316 ( 6) link_BETA1-4 : angle 1.23135 ( 18) hydrogen bonds : bond 0.04833 ( 929) hydrogen bonds : angle 4.44620 ( 2562) SS BOND : bond 0.00324 ( 41) SS BOND : angle 2.34435 ( 82) covalent geometry : bond 0.00364 (25612) covalent geometry : angle 0.53358 (34838) *********************** 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: 47 poor density : 205 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8026 (m-30) cc_final: 0.7765 (m-30) REVERT: C 129 LYS cc_start: 0.6982 (ttmm) cc_final: 0.6329 (pttt) REVERT: C 170 TYR cc_start: 0.7404 (t80) cc_final: 0.6792 (t80) REVERT: C 529 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8125 (mmmt) REVERT: C 977 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7554 (mp) REVERT: B 501 TYR cc_start: 0.7753 (m-10) cc_final: 0.7369 (m-10) REVERT: B 960 ASN cc_start: 0.7772 (m-40) cc_final: 0.7379 (t0) REVERT: B 977 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 394 ASN cc_start: 0.7004 (m-40) cc_final: 0.6545 (m-40) REVERT: A 460 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7300 (mtmm) REVERT: A 564 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7463 (mm-40) outliers start: 47 outliers final: 33 residues processed: 241 average time/residue: 0.3442 time to fit residues: 133.4613 Evaluate side-chains 234 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 375 PHE 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 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 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 752 LEU 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 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 547 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 C 519 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 675 GLN A 207 HIS A 239 GLN A 245 HIS A 409 GLN A 675 GLN A 901 GLN A 919 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110969 restraints weight = 28844.923| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.43 r_work: 0.2879 rms_B_bonded: 2.80 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: 0.7667 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 25694 Z= 0.320 Angle : 0.728 12.502 35043 Z= 0.371 Chirality : 0.050 0.216 4078 Planarity : 0.005 0.051 4451 Dihedral : 5.824 59.301 4212 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 1.87 % Allowed : 11.82 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3090 helix: 1.25 (0.20), residues: 703 sheet: 0.02 (0.19), residues: 654 loop : -1.58 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 436 HIS 0.009 0.002 HIS A1088 PHE 0.034 0.002 PHE C 377 TYR 0.026 0.002 TYR C 265 ARG 0.008 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 35) link_NAG-ASN : angle 2.47053 ( 105) link_BETA1-4 : bond 0.00295 ( 6) link_BETA1-4 : angle 1.56812 ( 18) hydrogen bonds : bond 0.06693 ( 929) hydrogen bonds : angle 4.89491 ( 2562) SS BOND : bond 0.00539 ( 41) SS BOND : angle 3.00322 ( 82) covalent geometry : bond 0.00805 (25612) covalent geometry : angle 0.70186 (34838) *********************** 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 259 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 53 ASP cc_start: 0.8112 (m-30) cc_final: 0.7881 (m-30) REVERT: C 129 LYS cc_start: 0.7150 (ttmm) cc_final: 0.6541 (pttt) REVERT: C 417 ASN cc_start: 0.7533 (m-40) cc_final: 0.7243 (t0) REVERT: C 529 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8169 (mmmt) REVERT: C 578 ASP cc_start: 0.8676 (t0) cc_final: 0.8220 (t0) REVERT: C 690 GLN cc_start: 0.7165 (mm110) cc_final: 0.6758 (mm110) REVERT: C 977 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 64 TRP cc_start: 0.6973 (t-100) cc_final: 0.6365 (t60) REVERT: B 501 TYR cc_start: 0.7765 (m-10) cc_final: 0.7449 (m-10) REVERT: B 960 ASN cc_start: 0.7939 (m-40) cc_final: 0.7561 (t0) REVERT: B 977 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 394 ASN cc_start: 0.7340 (m-40) cc_final: 0.6920 (m-40) REVERT: A 460 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7108 (mtmm) REVERT: A 568 ASP cc_start: 0.7001 (t0) cc_final: 0.6523 (t0) outliers start: 51 outliers final: 38 residues processed: 247 average time/residue: 0.3415 time to fit residues: 136.7570 Evaluate side-chains 241 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 433 VAL 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 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 42 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 430 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 752 LEU 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 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 409 GLN 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 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 247 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 211 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 278 optimal weight: 0.7980 chunk 310 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 239 GLN 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 = 0.3831 r_free = 0.3831 target = 0.163101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116192 restraints weight = 28540.597| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.54 r_work: 0.2920 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25694 Z= 0.131 Angle : 0.563 10.249 35043 Z= 0.287 Chirality : 0.044 0.240 4078 Planarity : 0.004 0.053 4451 Dihedral : 5.352 54.930 4212 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 1.62 % Allowed : 12.48 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3090 helix: 1.76 (0.20), residues: 698 sheet: 0.17 (0.20), residues: 651 loop : -1.46 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 PHE 0.032 0.001 PHE C 168 TYR 0.019 0.001 TYR A1067 ARG 0.011 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 35) link_NAG-ASN : angle 2.09550 ( 105) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 1.30918 ( 18) hydrogen bonds : bond 0.04841 ( 929) hydrogen bonds : angle 4.55992 ( 2562) SS BOND : bond 0.00293 ( 41) SS BOND : angle 2.38191 ( 82) covalent geometry : bond 0.00314 (25612) covalent geometry : angle 0.54012 (34838) *********************** 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 255 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8021 (m-30) cc_final: 0.7760 (m-30) REVERT: C 129 LYS cc_start: 0.7106 (ttmm) cc_final: 0.6510 (pttt) REVERT: C 417 ASN cc_start: 0.7434 (m-40) cc_final: 0.7122 (t0) REVERT: C 529 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8134 (mmmt) REVERT: C 578 ASP cc_start: 0.8654 (t0) cc_final: 0.8257 (t0) REVERT: C 690 GLN cc_start: 0.7246 (mm110) cc_final: 0.6899 (mm110) REVERT: C 977 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 64 TRP cc_start: 0.6797 (t-100) cc_final: 0.6262 (t60) REVERT: B 290 ASP cc_start: 0.8407 (t0) cc_final: 0.8194 (t0) REVERT: B 960 ASN cc_start: 0.7822 (m-40) cc_final: 0.7430 (t0) REVERT: B 977 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7684 (mp) REVERT: A 394 ASN cc_start: 0.7166 (m-40) cc_final: 0.6703 (m-40) REVERT: A 452 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6701 (pt) REVERT: A 495 TYR cc_start: 0.8272 (m-80) cc_final: 0.7978 (m-80) REVERT: A 564 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7460 (mm-40) REVERT: A 646 ARG cc_start: 0.8096 (tpt-90) cc_final: 0.6981 (tpp80) outliers start: 44 outliers final: 32 residues processed: 248 average time/residue: 0.3382 time to fit residues: 136.0905 Evaluate side-chains 238 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 433 VAL 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 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 430 THR Chi-restraints excluded: chain B residue 752 LEU 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 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 231 ILE 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 524 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 111 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 233 optimal weight: 0.0570 chunk 222 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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 239 GLN A 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114034 restraints weight = 28375.318| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.46 r_work: 0.2965 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25694 Z= 0.110 Angle : 0.539 10.187 35043 Z= 0.272 Chirality : 0.044 0.243 4078 Planarity : 0.003 0.053 4451 Dihedral : 5.018 54.263 4212 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 1.43 % Allowed : 12.74 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3090 helix: 2.12 (0.20), residues: 689 sheet: 0.24 (0.19), residues: 663 loop : -1.34 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 PHE 0.030 0.001 PHE C 168 TYR 0.016 0.001 TYR A1067 ARG 0.009 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 35) link_NAG-ASN : angle 1.94069 ( 105) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 1.24264 ( 18) hydrogen bonds : bond 0.04344 ( 929) hydrogen bonds : angle 4.40133 ( 2562) SS BOND : bond 0.00304 ( 41) SS BOND : angle 2.25195 ( 82) covalent geometry : bond 0.00257 (25612) covalent geometry : angle 0.51778 (34838) ********************** 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 237 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8054 (m-30) cc_final: 0.7785 (m-30) REVERT: C 129 LYS cc_start: 0.7074 (ttmm) cc_final: 0.6413 (pttt) REVERT: C 417 ASN cc_start: 0.7541 (m-40) cc_final: 0.7220 (t0) REVERT: C 578 ASP cc_start: 0.8646 (t0) cc_final: 0.8288 (t0) REVERT: C 690 GLN cc_start: 0.7250 (mm110) cc_final: 0.6931 (mm110) REVERT: C 977 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7879 (mp) REVERT: B 64 TRP cc_start: 0.6918 (t-100) cc_final: 0.6341 (t60) REVERT: B 960 ASN cc_start: 0.7878 (m-40) cc_final: 0.7460 (t0) REVERT: B 977 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7709 (mp) REVERT: A 394 ASN cc_start: 0.7139 (m-40) cc_final: 0.6717 (m-40) REVERT: A 452 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6879 (pt) REVERT: A 532 ASN cc_start: 0.8234 (t0) cc_final: 0.8027 (t0) REVERT: A 564 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7521 (mm-40) outliers start: 39 outliers final: 33 residues processed: 230 average time/residue: 0.3524 time to fit residues: 131.8682 Evaluate side-chains 231 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 433 VAL 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 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 752 LEU 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 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 231 ILE 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 524 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 101 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 675 GLN A 207 HIS A 239 GLN A 493 GLN A 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114067 restraints weight = 28585.286| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.45 r_work: 0.2924 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25694 Z= 0.179 Angle : 0.600 10.013 35043 Z= 0.303 Chirality : 0.046 0.230 4078 Planarity : 0.004 0.051 4451 Dihedral : 5.239 53.048 4212 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 1.51 % Allowed : 12.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3090 helix: 1.73 (0.20), residues: 707 sheet: 0.17 (0.19), residues: 653 loop : -1.42 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS A1058 PHE 0.028 0.002 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.009 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 35) link_NAG-ASN : angle 2.08084 ( 105) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.30629 ( 18) hydrogen bonds : bond 0.05230 ( 929) hydrogen bonds : angle 4.57116 ( 2562) SS BOND : bond 0.00374 ( 41) SS BOND : angle 2.53232 ( 82) covalent geometry : bond 0.00442 (25612) covalent geometry : angle 0.57709 (34838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14672.71 seconds wall clock time: 253 minutes 41.43 seconds (15221.43 seconds total)