Starting phenix.real_space_refine on Sat May 24 13:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0x_34417/05_2025/8h0x_34417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0x_34417/05_2025/8h0x_34417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0x_34417/05_2025/8h0x_34417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0x_34417/05_2025/8h0x_34417.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0x_34417/05_2025/8h0x_34417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0x_34417/05_2025/8h0x_34417.cif" } resolution = 2.57 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= 0.007 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 141 5.16 5 C 16062 2.51 5 N 4083 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.67s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25122 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8115 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 5 Chain: "B" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8115 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 5 Chain: "C" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8115 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 5 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 279 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLA': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 14.41, per 1000 atoms: 0.57 Number of scatterers: 25122 At special positions: 0 Unit cell: (124.83, 136.875, 173.01, 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 141 16.00 O 4836 8.00 N 4083 7.00 C 16062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS B 967 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.06 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.05 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS C 967 " distance=2.06 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.05 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 65 " " NAG A1303 " - " ASN A1080 " " NAG A1304 " - " ASN A 109 " " NAG A1305 " - " ASN A 119 " " NAG A1306 " - " ASN A 158 " " NAG A1307 " - " ASN A 227 " " NAG A1308 " - " ASN A 269 " " NAG A1309 " - " ASN A 318 " " NAG A1310 " - " ASN A 330 " " NAG A1311 " - " ASN A 357 " " NAG A1312 " - " ASN A 602 " " NAG A1313 " - " ASN A 699 " " NAG A1314 " - " ASN A 783 " " NAG A1315 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 227 " " NAG B1307 " - " ASN B 269 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 330 " " NAG B1310 " - " ASN B 357 " " NAG B1311 " - " ASN B 602 " " NAG B1312 " - " ASN B 699 " " NAG B1313 " - " ASN B 783 " " NAG B1314 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 109 " " NAG C1304 " - " ASN C 119 " " NAG C1305 " - " ASN C 158 " " NAG C1306 " - " ASN C 227 " " NAG C1307 " - " ASN C 269 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 330 " " NAG C1310 " - " ASN C 357 " " NAG C1311 " - " ASN C 602 " " NAG C1312 " - " ASN C 699 " " NAG C1313 " - " ASN C 783 " " NAG C1314 " - " ASN C1116 " Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 3.0 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 25.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.598A pdb=" N LEU A 355 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.511A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.669A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 738 through 765 removed outlier: 3.671A pdb=" N CYS A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.833A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 830 through 837 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.620A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.150A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.593A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.515A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.648A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.598A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.512A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.668A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 738 through 765 removed outlier: 3.672A pdb=" N CYS B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.833A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 830 through 837 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.620A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.150A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.593A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.514A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.648A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.598A pdb=" N LEU C 355 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.511A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.668A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 738 through 765 removed outlier: 3.672A pdb=" N CYS C 742 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.833A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 825 Processing helix chain 'C' and resid 830 through 837 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 891 removed outlier: 3.621A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.150A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.592A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.515A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.647A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.441A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 5.305A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY C 311 " --> pdb=" O CYS C 524 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.095A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.739A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 13.965A pdb=" N PHE A 231 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ASP A 134 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ALA A 233 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 235 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.071A pdb=" N GLY A 311 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.255A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.597A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 510 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 435 through 441 removed outlier: 5.894A pdb=" N TYR A 436 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE A 483 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.144A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.501A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.663A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.663A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.493A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB8, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.549A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.441A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.096A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.739A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.071A pdb=" N GLY B 311 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.255A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.598A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 510 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 435 through 441 removed outlier: 5.893A pdb=" N TYR B 436 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE B 483 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR B 438 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.143A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.788A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.663A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.663A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.493A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.549A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.441A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.096A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.739A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU C 131 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N PHE C 157 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.255A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.597A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 510 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 435 through 441 removed outlier: 5.894A pdb=" N TYR C 436 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE C 483 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.143A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.663A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.663A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.494A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 778 through 779 removed outlier: 3.549A pdb=" N PHE C 782 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1102 through 1104 1059 hydrogen bonds defined for protein. 2937 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: 12.77 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4071 1.31 - 1.45: 7474 1.45 - 1.59: 13964 1.59 - 1.73: 0 1.73 - 1.86: 189 Bond restraints: 25698 Sorted by residual: bond pdb=" ND BLA A1316 " pdb=" C1D BLA A1316 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" ND BLA B1315 " pdb=" C1D BLA B1315 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" ND BLA C1315 " pdb=" C1D BLA C1315 " ideal model delta sigma weight residual 1.319 1.480 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C1C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.368 1.529 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" C1C BLA A1316 " pdb=" NC BLA A1316 " ideal model delta sigma weight residual 1.368 1.529 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 25693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 34728 4.21 - 8.42: 185 8.42 - 12.63: 19 12.63 - 16.84: 0 16.84 - 21.05: 3 Bond angle restraints: 34935 Sorted by residual: angle pdb=" CB MET C 884 " pdb=" CG MET C 884 " pdb=" SD MET C 884 " ideal model delta sigma weight residual 112.70 133.75 -21.05 3.00e+00 1.11e-01 4.92e+01 angle pdb=" CB MET A 884 " pdb=" CG MET A 884 " pdb=" SD MET A 884 " ideal model delta sigma weight residual 112.70 133.74 -21.04 3.00e+00 1.11e-01 4.92e+01 angle pdb=" CB MET B 884 " pdb=" CG MET B 884 " pdb=" SD MET B 884 " ideal model delta sigma weight residual 112.70 133.68 -20.98 3.00e+00 1.11e-01 4.89e+01 angle pdb=" C CYS A 967 " pdb=" CA CYS A 967 " pdb=" CB CYS A 967 " ideal model delta sigma weight residual 109.66 118.70 -9.04 1.94e+00 2.66e-01 2.17e+01 angle pdb=" C THR A 150 " pdb=" N MET A 151 " pdb=" CA MET A 151 " ideal model delta sigma weight residual 123.11 116.50 6.61 1.42e+00 4.96e-01 2.17e+01 ... (remaining 34930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 14654 17.44 - 34.89: 864 34.89 - 52.33: 245 52.33 - 69.78: 41 69.78 - 87.22: 39 Dihedral angle restraints: 15843 sinusoidal: 6768 harmonic: 9075 Sorted by residual: dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual 93.00 6.09 86.91 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual 93.00 6.10 86.90 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual 93.00 6.12 86.88 1 1.00e+01 1.00e-02 9.08e+01 ... (remaining 15840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3784 0.107 - 0.215: 220 0.215 - 0.322: 13 0.322 - 0.429: 6 0.429 - 0.536: 6 Chirality restraints: 4029 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 699 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" C1 NAG A1313 " pdb=" ND2 ASN A 699 " pdb=" C2 NAG A1313 " pdb=" O5 NAG A1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" C1 NAG B1312 " pdb=" ND2 ASN B 699 " pdb=" C2 NAG B1312 " pdb=" O5 NAG B1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.08e+00 ... (remaining 4026 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1316 " -0.014 2.00e-02 2.50e+03 8.75e-02 1.92e+02 pdb=" C1D BLA A1316 " 0.198 2.00e-02 2.50e+03 pdb=" C2C BLA A1316 " 0.020 2.00e-02 2.50e+03 pdb=" C3C BLA A1316 " -0.014 2.00e-02 2.50e+03 pdb=" C4C BLA A1316 " -0.079 2.00e-02 2.50e+03 pdb=" CAC BLA A1316 " 0.001 2.00e-02 2.50e+03 pdb=" CHD BLA A1316 " -0.127 2.00e-02 2.50e+03 pdb=" CMC BLA A1316 " 0.088 2.00e-02 2.50e+03 pdb=" NC BLA A1316 " -0.078 2.00e-02 2.50e+03 pdb=" OC BLA A1316 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1315 " -0.014 2.00e-02 2.50e+03 8.74e-02 1.91e+02 pdb=" C1D BLA B1315 " 0.198 2.00e-02 2.50e+03 pdb=" C2C BLA B1315 " 0.021 2.00e-02 2.50e+03 pdb=" C3C BLA B1315 " -0.014 2.00e-02 2.50e+03 pdb=" C4C BLA B1315 " -0.078 2.00e-02 2.50e+03 pdb=" CAC BLA B1315 " 0.001 2.00e-02 2.50e+03 pdb=" CHD BLA B1315 " -0.128 2.00e-02 2.50e+03 pdb=" CMC BLA B1315 " 0.088 2.00e-02 2.50e+03 pdb=" NC BLA B1315 " -0.079 2.00e-02 2.50e+03 pdb=" OC BLA B1315 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA C1315 " -0.013 2.00e-02 2.50e+03 8.74e-02 1.91e+02 pdb=" C1D BLA C1315 " 0.198 2.00e-02 2.50e+03 pdb=" C2C BLA C1315 " 0.020 2.00e-02 2.50e+03 pdb=" C3C BLA C1315 " -0.014 2.00e-02 2.50e+03 pdb=" C4C BLA C1315 " -0.079 2.00e-02 2.50e+03 pdb=" CAC BLA C1315 " 0.001 2.00e-02 2.50e+03 pdb=" CHD BLA C1315 " -0.127 2.00e-02 2.50e+03 pdb=" CMC BLA C1315 " 0.088 2.00e-02 2.50e+03 pdb=" NC BLA C1315 " -0.079 2.00e-02 2.50e+03 pdb=" OC BLA C1315 " 0.005 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5424 2.79 - 3.31: 20522 3.31 - 3.84: 39075 3.84 - 4.37: 47565 4.37 - 4.90: 82977 Nonbonded interactions: 195563 Sorted by model distance: nonbonded pdb=" N ASN A 589 " pdb=" OD1 ASN A 589 " model vdw 2.257 3.120 nonbonded pdb=" N ASN B 589 " pdb=" OD1 ASN B 589 " model vdw 2.257 3.120 nonbonded pdb=" N ASN C 589 " pdb=" OD1 ASN C 589 " model vdw 2.257 3.120 nonbonded pdb=" OG SER A 461 " pdb=" OD1 ASP A 463 " model vdw 2.282 3.040 nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 463 " model vdw 2.282 3.040 ... (remaining 195558 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 31 through 1123 or resid 1302 through 1314)) selection = (chain 'B' and (resid 31 through 1123 or resid 1302 through 1314)) selection = (chain 'C' and (resid 31 through 1123 or resid 1302 through 1314)) } 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=0.00 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: 0.010 Normalize map: mean=0, sd=1: 2.110 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: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 57.780 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.008 0.162 25785 Z= 0.379 Angle : 0.961 21.053 35151 Z= 0.508 Chirality : 0.059 0.536 4029 Planarity : 0.006 0.088 4458 Dihedral : 12.824 87.220 9876 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.11 % Allowed : 1.48 % Favored : 97.40 % 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: -0.82 (0.14), residues: 3081 helix: 0.22 (0.19), residues: 696 sheet: 1.07 (0.20), residues: 669 loop : -1.61 (0.12), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 868 HIS 0.005 0.001 HIS A1046 PHE 0.057 0.002 PHE B 334 TYR 0.037 0.002 TYR C 886 ARG 0.042 0.001 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 42) link_NAG-ASN : angle 3.92611 ( 126) hydrogen bonds : bond 0.14447 ( 1011) hydrogen bonds : angle 6.20508 ( 2937) SS BOND : bond 0.00987 ( 45) SS BOND : angle 2.29216 ( 90) covalent geometry : bond 0.00788 (25698) covalent geometry : angle 0.92778 (34935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 2.608 Fit side-chains REVERT: A 685 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7483 (m) REVERT: B 151 MET cc_start: 0.6690 (mmt) cc_final: 0.6395 (mmt) REVERT: B 884 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8569 (mmm) REVERT: C 137 PHE cc_start: 0.8511 (p90) cc_final: 0.8110 (p90) REVERT: C 151 MET cc_start: 0.7007 (mmt) cc_final: 0.6479 (mmt) REVERT: C 685 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7438 (m) outliers start: 30 outliers final: 7 residues processed: 273 average time/residue: 1.4427 time to fit residues: 450.8077 Evaluate side-chains 170 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 685 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.9990 chunk 234 optimal weight: 0.0370 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS B 626 ASN C 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092337 restraints weight = 32286.861| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.09 r_work: 0.2976 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25785 Z= 0.118 Angle : 0.582 14.043 35151 Z= 0.302 Chirality : 0.047 0.341 4029 Planarity : 0.004 0.064 4458 Dihedral : 7.645 68.939 4373 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.15 % Allowed : 6.38 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.30 (0.14), residues: 3081 helix: 1.34 (0.20), residues: 678 sheet: 1.14 (0.19), residues: 702 loop : -1.53 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 868 HIS 0.004 0.001 HIS A 181 PHE 0.011 0.001 PHE A 137 TYR 0.018 0.001 TYR A1120 ARG 0.006 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 42) link_NAG-ASN : angle 2.45543 ( 126) hydrogen bonds : bond 0.05476 ( 1011) hydrogen bonds : angle 5.17144 ( 2937) SS BOND : bond 0.00589 ( 45) SS BOND : angle 1.70567 ( 90) covalent geometry : bond 0.00249 (25698) covalent geometry : angle 0.55793 (34935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 2.640 Fit side-chains REVERT: A 544 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8341 (ptp90) REVERT: A 769 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: B 518 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8195 (t0) REVERT: B 884 MET cc_start: 0.9055 (mmm) cc_final: 0.8823 (tpt) REVERT: C 130 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.5524 (p90) REVERT: C 137 PHE cc_start: 0.8142 (p90) cc_final: 0.7928 (p90) REVERT: C 151 MET cc_start: 0.7421 (mmt) cc_final: 0.7099 (mmt) outliers start: 31 outliers final: 11 residues processed: 201 average time/residue: 1.2590 time to fit residues: 296.7188 Evaluate side-chains 168 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 109 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 626 ASN B 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.089746 restraints weight = 32235.409| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.00 r_work: 0.2902 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25785 Z= 0.180 Angle : 0.664 17.704 35151 Z= 0.343 Chirality : 0.051 0.409 4029 Planarity : 0.005 0.057 4458 Dihedral : 7.261 61.351 4362 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.86 % Allowed : 7.76 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % 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: -0.30 (0.14), residues: 3081 helix: 1.44 (0.21), residues: 681 sheet: 1.10 (0.19), residues: 678 loop : -1.52 (0.12), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 868 HIS 0.006 0.001 HIS A1046 PHE 0.017 0.002 PHE C 870 TYR 0.022 0.002 TYR B1049 ARG 0.005 0.001 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 42) link_NAG-ASN : angle 2.49468 ( 126) hydrogen bonds : bond 0.06771 ( 1011) hydrogen bonds : angle 5.27591 ( 2937) SS BOND : bond 0.00890 ( 45) SS BOND : angle 2.49512 ( 90) covalent geometry : bond 0.00427 (25698) covalent geometry : angle 0.63642 (34935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 2.793 Fit side-chains REVERT: A 709 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.9141 (mtp) REVERT: A 816 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7940 (tpp) REVERT: B 267 ASP cc_start: 0.8456 (m-30) cc_final: 0.8185 (m-30) REVERT: B 296 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: B 518 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8390 (t0) REVERT: C 130 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.5287 (p90) REVERT: C 137 PHE cc_start: 0.8295 (p90) cc_final: 0.8005 (p90) REVERT: C 151 MET cc_start: 0.7296 (mmt) cc_final: 0.7041 (mmt) outliers start: 50 outliers final: 22 residues processed: 209 average time/residue: 1.2089 time to fit residues: 297.7922 Evaluate side-chains 181 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 966 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 177 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 99 optimal weight: 0.0170 chunk 152 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 236 optimal weight: 0.0980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 626 ASN B 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089086 restraints weight = 32484.733| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.07 r_work: 0.2902 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25785 Z= 0.161 Angle : 0.639 18.853 35151 Z= 0.328 Chirality : 0.049 0.376 4029 Planarity : 0.004 0.054 4458 Dihedral : 7.023 59.299 4360 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.08 % Allowed : 8.76 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.22 (0.14), residues: 3081 helix: 1.55 (0.21), residues: 681 sheet: 1.09 (0.19), residues: 678 loop : -1.45 (0.12), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 PHE 0.014 0.001 PHE B 870 TYR 0.020 0.002 TYR B1049 ARG 0.006 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 42) link_NAG-ASN : angle 2.30286 ( 126) hydrogen bonds : bond 0.06191 ( 1011) hydrogen bonds : angle 5.19915 ( 2937) SS BOND : bond 0.00797 ( 45) SS BOND : angle 2.68529 ( 90) covalent geometry : bond 0.00381 (25698) covalent geometry : angle 0.61053 (34935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 2.749 Fit side-chains REVERT: A 426 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7889 (ttm-80) REVERT: A 708 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (m) REVERT: A 709 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9030 (mtp) REVERT: A 816 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: B 130 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7117 (p90) REVERT: B 267 ASP cc_start: 0.8479 (m-30) cc_final: 0.8199 (m-30) REVERT: B 792 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 816 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8483 (ttp) REVERT: B 884 MET cc_start: 0.9154 (mmt) cc_final: 0.8864 (tpt) REVERT: C 130 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.5544 (p90) REVERT: C 137 PHE cc_start: 0.8349 (p90) cc_final: 0.8074 (p90) outliers start: 56 outliers final: 30 residues processed: 211 average time/residue: 1.2154 time to fit residues: 302.3954 Evaluate side-chains 192 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 176 optimal weight: 0.9990 chunk 281 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090190 restraints weight = 32454.724| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.00 r_work: 0.2898 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25785 Z= 0.138 Angle : 0.621 16.543 35151 Z= 0.314 Chirality : 0.048 0.347 4029 Planarity : 0.004 0.053 4458 Dihedral : 6.738 54.887 4360 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.19 % Allowed : 9.69 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3081 helix: 1.66 (0.21), residues: 681 sheet: 1.09 (0.19), residues: 672 loop : -1.38 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 868 HIS 0.004 0.001 HIS A1046 PHE 0.012 0.001 PHE B 870 TYR 0.019 0.001 TYR B1049 ARG 0.005 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 42) link_NAG-ASN : angle 2.16153 ( 126) hydrogen bonds : bond 0.05764 ( 1011) hydrogen bonds : angle 5.11105 ( 2937) SS BOND : bond 0.00644 ( 45) SS BOND : angle 2.74574 ( 90) covalent geometry : bond 0.00318 (25698) covalent geometry : angle 0.59330 (34935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 2.629 Fit side-chains REVERT: A 306 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7787 (ptp90) REVERT: A 426 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: A 709 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.9056 (mtp) REVERT: A 816 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7854 (tpp) REVERT: A 825 ASP cc_start: 0.6409 (m-30) cc_final: 0.6194 (t0) REVERT: B 130 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7375 (p90) REVERT: B 267 ASP cc_start: 0.8479 (m-30) cc_final: 0.8195 (m-30) REVERT: B 708 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8883 (m) REVERT: B 792 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (tt) REVERT: B 796 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7881 (mmtm) REVERT: B 816 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: B 884 MET cc_start: 0.9148 (mmt) cc_final: 0.8816 (tpt) REVERT: C 130 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.5620 (p90) REVERT: C 137 PHE cc_start: 0.8416 (p90) cc_final: 0.8196 (p90) REVERT: C 593 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8207 (mm-30) outliers start: 59 outliers final: 30 residues processed: 204 average time/residue: 1.2011 time to fit residues: 292.5974 Evaluate side-chains 197 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 308 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 252 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089256 restraints weight = 32312.896| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.00 r_work: 0.2909 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25785 Z= 0.156 Angle : 0.635 16.962 35151 Z= 0.322 Chirality : 0.049 0.360 4029 Planarity : 0.004 0.052 4458 Dihedral : 6.606 54.709 4360 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.60 % Allowed : 9.47 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -0.18 (0.14), residues: 3081 helix: 1.67 (0.21), residues: 681 sheet: 0.98 (0.19), residues: 702 loop : -1.44 (0.12), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 PHE 0.014 0.001 PHE B 870 TYR 0.022 0.002 TYR B1120 ARG 0.004 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 42) link_NAG-ASN : angle 2.18610 ( 126) hydrogen bonds : bond 0.06170 ( 1011) hydrogen bonds : angle 5.15656 ( 2937) SS BOND : bond 0.00688 ( 45) SS BOND : angle 2.63039 ( 90) covalent geometry : bond 0.00368 (25698) covalent geometry : angle 0.60832 (34935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 159 time to evaluate : 2.707 Fit side-chains REVERT: A 130 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7214 (p90) REVERT: A 426 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7881 (ttm-80) REVERT: A 708 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8901 (m) REVERT: A 709 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.9051 (mtp) REVERT: A 816 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7816 (tpp) REVERT: B 130 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7465 (p90) REVERT: B 267 ASP cc_start: 0.8458 (m-30) cc_final: 0.8169 (m-30) REVERT: B 426 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7751 (ttm-80) REVERT: B 792 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8082 (tt) REVERT: B 796 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7915 (mmtm) REVERT: B 816 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8460 (ttp) REVERT: C 32 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: C 130 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.5561 (p90) REVERT: C 137 PHE cc_start: 0.8510 (p90) cc_final: 0.8301 (p90) REVERT: C 426 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7542 (ttm-80) REVERT: C 593 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8105 (mm-30) outliers start: 70 outliers final: 30 residues processed: 208 average time/residue: 1.2245 time to fit residues: 299.8276 Evaluate side-chains 195 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 426 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 24 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 279 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN C 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.088719 restraints weight = 32431.501| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.08 r_work: 0.2877 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25785 Z= 0.161 Angle : 0.632 16.972 35151 Z= 0.320 Chirality : 0.049 0.367 4029 Planarity : 0.004 0.052 4458 Dihedral : 6.511 54.652 4358 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.64 % Allowed : 9.84 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3081 helix: 1.50 (0.20), residues: 699 sheet: 1.09 (0.19), residues: 672 loop : -1.46 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 PHE 0.013 0.001 PHE A 870 TYR 0.020 0.002 TYR B1049 ARG 0.004 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 42) link_NAG-ASN : angle 2.21869 ( 126) hydrogen bonds : bond 0.06217 ( 1011) hydrogen bonds : angle 5.15229 ( 2937) SS BOND : bond 0.00680 ( 45) SS BOND : angle 2.55096 ( 90) covalent geometry : bond 0.00382 (25698) covalent geometry : angle 0.60649 (34935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 2.675 Fit side-chains REVERT: A 151 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5274 (mpt) REVERT: A 426 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7938 (ttm-80) REVERT: A 708 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8912 (m) REVERT: A 709 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9091 (mtp) REVERT: A 816 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7954 (tpp) REVERT: B 130 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7520 (p90) REVERT: B 267 ASP cc_start: 0.8444 (m-30) cc_final: 0.8161 (m-30) REVERT: B 426 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7748 (ttm-80) REVERT: B 792 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 796 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7940 (mmtm) REVERT: B 816 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8469 (ttp) REVERT: B 825 ASP cc_start: 0.6511 (m-30) cc_final: 0.6244 (t0) REVERT: B 884 MET cc_start: 0.9188 (tpt) cc_final: 0.8786 (tpt) REVERT: C 130 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7011 (p90) REVERT: C 322 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 593 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8165 (mm-30) REVERT: C 708 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8846 (t) outliers start: 71 outliers final: 40 residues processed: 211 average time/residue: 1.2714 time to fit residues: 314.9618 Evaluate side-chains 208 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 265 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 281 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.090772 restraints weight = 32358.796| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.97 r_work: 0.2912 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25785 Z= 0.130 Angle : 0.601 18.200 35151 Z= 0.303 Chirality : 0.047 0.330 4029 Planarity : 0.004 0.051 4458 Dihedral : 6.264 52.291 4358 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 10.32 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3081 helix: 1.78 (0.21), residues: 681 sheet: 1.02 (0.19), residues: 702 loop : -1.37 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 PHE 0.011 0.001 PHE B 870 TYR 0.020 0.001 TYR B1120 ARG 0.004 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 42) link_NAG-ASN : angle 2.06393 ( 126) hydrogen bonds : bond 0.05563 ( 1011) hydrogen bonds : angle 5.04888 ( 2937) SS BOND : bond 0.00541 ( 45) SS BOND : angle 2.54719 ( 90) covalent geometry : bond 0.00297 (25698) covalent geometry : angle 0.57527 (34935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 2.813 Fit side-chains REVERT: A 426 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: A 685 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7224 (p) REVERT: A 708 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8853 (t) REVERT: A 709 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9079 (mtp) REVERT: A 816 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7927 (tpp) REVERT: B 129 ASN cc_start: 0.8252 (t0) cc_final: 0.8045 (t0) REVERT: B 130 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7522 (p90) REVERT: B 267 ASP cc_start: 0.8378 (m-30) cc_final: 0.8132 (m-30) REVERT: B 792 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 796 LYS cc_start: 0.8258 (mmmt) cc_final: 0.8019 (mmtm) REVERT: B 825 ASP cc_start: 0.6518 (m-30) cc_final: 0.6249 (t0) REVERT: B 884 MET cc_start: 0.9193 (tpt) cc_final: 0.8763 (tpt) REVERT: C 130 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7196 (p90) REVERT: C 708 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8845 (t) outliers start: 57 outliers final: 37 residues processed: 205 average time/residue: 1.2315 time to fit residues: 299.4580 Evaluate side-chains 203 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 239 optimal weight: 0.0770 chunk 39 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN B 936 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088996 restraints weight = 32476.687| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.09 r_work: 0.2875 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25785 Z= 0.158 Angle : 0.656 19.416 35151 Z= 0.330 Chirality : 0.049 0.353 4029 Planarity : 0.004 0.051 4458 Dihedral : 6.374 54.324 4358 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 10.43 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -0.16 (0.14), residues: 3081 helix: 1.55 (0.20), residues: 699 sheet: 1.13 (0.19), residues: 672 loop : -1.42 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 PHE 0.013 0.001 PHE A 870 TYR 0.020 0.002 TYR B1049 ARG 0.004 0.000 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 42) link_NAG-ASN : angle 2.13929 ( 126) hydrogen bonds : bond 0.06118 ( 1011) hydrogen bonds : angle 5.13697 ( 2937) SS BOND : bond 0.00686 ( 45) SS BOND : angle 3.13822 ( 90) covalent geometry : bond 0.00372 (25698) covalent geometry : angle 0.62491 (34935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 3.025 Fit side-chains REVERT: A 426 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7946 (ttm-80) REVERT: A 685 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7218 (p) REVERT: A 708 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8910 (m) REVERT: A 709 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.9096 (mtp) REVERT: A 816 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7965 (tpp) REVERT: B 130 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7507 (p90) REVERT: B 267 ASP cc_start: 0.8407 (m-30) cc_final: 0.8151 (m-30) REVERT: B 792 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 796 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8093 (mmtm) REVERT: B 816 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8493 (ttp) REVERT: B 825 ASP cc_start: 0.6517 (m-30) cc_final: 0.6262 (t0) REVERT: C 130 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7023 (p90) outliers start: 57 outliers final: 41 residues processed: 201 average time/residue: 1.1916 time to fit residues: 282.8053 Evaluate side-chains 209 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1108 CYS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 215 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 chunk 226 optimal weight: 0.5980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.090663 restraints weight = 32325.256| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.04 r_work: 0.2935 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25785 Z= 0.121 Angle : 0.614 18.285 35151 Z= 0.309 Chirality : 0.047 0.321 4029 Planarity : 0.004 0.050 4458 Dihedral : 6.202 50.943 4358 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.74 % Allowed : 10.99 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.20 % 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: -0.03 (0.14), residues: 3081 helix: 1.82 (0.21), residues: 681 sheet: 1.09 (0.20), residues: 672 loop : -1.32 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 868 HIS 0.003 0.001 HIS A 181 PHE 0.009 0.001 PHE B 870 TYR 0.022 0.001 TYR B1120 ARG 0.003 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 42) link_NAG-ASN : angle 2.00947 ( 126) hydrogen bonds : bond 0.05361 ( 1011) hydrogen bonds : angle 5.04005 ( 2937) SS BOND : bond 0.00560 ( 45) SS BOND : angle 2.99416 ( 90) covalent geometry : bond 0.00270 (25698) covalent geometry : angle 0.58403 (34935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 3.057 Fit side-chains REVERT: A 426 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7900 (ttm-80) REVERT: A 685 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 709 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9069 (mtp) REVERT: A 816 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7880 (tpp) REVERT: B 129 ASN cc_start: 0.8213 (t0) cc_final: 0.8009 (t0) REVERT: B 130 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7562 (p90) REVERT: B 267 ASP cc_start: 0.8320 (m-30) cc_final: 0.8095 (m-30) REVERT: B 792 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8086 (tt) REVERT: B 796 LYS cc_start: 0.8308 (mmmt) cc_final: 0.8093 (mmtm) REVERT: B 884 MET cc_start: 0.9155 (tpt) cc_final: 0.8881 (tpt) REVERT: C 130 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7213 (p90) REVERT: C 708 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8837 (t) outliers start: 47 outliers final: 31 residues processed: 193 average time/residue: 1.2034 time to fit residues: 277.6271 Evaluate side-chains 193 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 55 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 173 optimal weight: 0.0020 chunk 161 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.090612 restraints weight = 32328.195| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.07 r_work: 0.2907 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25785 Z= 0.124 Angle : 0.615 17.932 35151 Z= 0.310 Chirality : 0.047 0.318 4029 Planarity : 0.004 0.051 4458 Dihedral : 6.142 50.653 4358 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.97 % Allowed : 10.80 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3081 helix: 1.72 (0.20), residues: 696 sheet: 1.08 (0.19), residues: 672 loop : -1.38 (0.12), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 868 HIS 0.003 0.001 HIS A1046 PHE 0.010 0.001 PHE A 137 TYR 0.020 0.001 TYR C1120 ARG 0.003 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 42) link_NAG-ASN : angle 1.98330 ( 126) hydrogen bonds : bond 0.05388 ( 1011) hydrogen bonds : angle 5.01446 ( 2937) SS BOND : bond 0.00565 ( 45) SS BOND : angle 3.00129 ( 90) covalent geometry : bond 0.00281 (25698) covalent geometry : angle 0.58567 (34935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16936.11 seconds wall clock time: 292 minutes 33.65 seconds (17553.65 seconds total)