Starting phenix.real_space_refine on Mon Aug 25 05:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0x_34417/08_2025/8h0x_34417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0x_34417/08_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_34417/08_2025/8h0x_34417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0x_34417/08_2025/8h0x_34417.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0x_34417/08_2025/8h0x_34417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0x_34417/08_2025/8h0x_34417.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.99, per 1000 atoms: 0.24 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: 1.51 Conformation dependent library (CDL) restraints added in 995.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.85 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: 5.76 Time building geometry restraints manager: 2.17 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: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.930 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (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 ARG 0.042 0.001 ARG A 306 TYR 0.037 0.002 TYR C 886 PHE 0.057 0.002 PHE B 334 TRP 0.043 0.003 TRP C 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00788 (25698) covalent geometry : angle 0.92778 (34935) SS BOND : bond 0.00987 ( 45) SS BOND : angle 2.29216 ( 90) hydrogen bonds : bond 0.14447 ( 1011) hydrogen bonds : angle 6.20508 ( 2937) link_NAG-ASN : bond 0.00566 ( 42) link_NAG-ASN : angle 3.92611 ( 126) *********************** 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 : 0.894 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: 0.7087 time to fit residues: 220.2332 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 : 0.788 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN C 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092821 restraints weight = 32309.326| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.02 r_work: 0.2956 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25785 Z= 0.132 Angle : 0.594 15.319 35151 Z= 0.308 Chirality : 0.048 0.366 4029 Planarity : 0.005 0.062 4458 Dihedral : 7.535 66.514 4373 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.45 % Allowed : 6.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3081 helix: 1.33 (0.21), residues: 678 sheet: 1.04 (0.19), residues: 693 loop : -1.51 (0.13), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 544 TYR 0.019 0.001 TYR A1120 PHE 0.014 0.001 PHE C 334 TRP 0.018 0.001 TRP A 868 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00294 (25698) covalent geometry : angle 0.57091 (34935) SS BOND : bond 0.00643 ( 45) SS BOND : angle 1.75644 ( 90) hydrogen bonds : bond 0.05658 ( 1011) hydrogen bonds : angle 5.18800 ( 2937) link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 2.41265 ( 126) *********************** 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 223 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.953 Fit side-chains REVERT: A 544 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8313 (ptp90) REVERT: A 769 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: B 518 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8198 (t0) REVERT: B 769 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: C 130 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.5433 (p90) REVERT: C 151 MET cc_start: 0.7342 (mmt) cc_final: 0.6990 (mmt) outliers start: 39 outliers final: 13 residues processed: 204 average time/residue: 0.6035 time to fit residues: 143.3804 Evaluate side-chains 169 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 433 THR 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 B residue 736 LEU Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 736 LEU 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 224 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.087405 restraints weight = 32413.320| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.11 r_work: 0.2857 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25785 Z= 0.216 Angle : 0.703 17.335 35151 Z= 0.363 Chirality : 0.053 0.439 4029 Planarity : 0.005 0.056 4458 Dihedral : 7.455 61.372 4360 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 7.87 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3081 helix: 1.34 (0.20), residues: 678 sheet: 1.06 (0.19), residues: 678 loop : -1.54 (0.12), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1021 TYR 0.023 0.002 TYR B1049 PHE 0.019 0.002 PHE A 870 TRP 0.022 0.002 TRP A 868 HIS 0.007 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00525 (25698) covalent geometry : angle 0.67470 (34935) SS BOND : bond 0.00836 ( 45) SS BOND : angle 2.56691 ( 90) hydrogen bonds : bond 0.07332 ( 1011) hydrogen bonds : angle 5.37509 ( 2937) link_NAG-ASN : bond 0.00400 ( 42) link_NAG-ASN : angle 2.60972 ( 126) *********************** 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 230 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.996 Fit side-chains REVERT: A 709 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.9199 (mtp) REVERT: A 816 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: B 267 ASP cc_start: 0.8499 (m-30) cc_final: 0.8180 (m-30) REVERT: B 816 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8457 (ttp) REVERT: B 1107 ASN cc_start: 0.8835 (p0) cc_final: 0.8573 (p0) REVERT: C 32 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: C 130 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.5566 (p90) REVERT: C 137 PHE cc_start: 0.8241 (p90) cc_final: 0.8019 (p90) REVERT: C 151 MET cc_start: 0.7510 (mmt) cc_final: 0.7256 (mmt) REVERT: C 825 ASP cc_start: 0.6820 (m-30) cc_final: 0.6475 (t0) outliers start: 54 outliers final: 24 residues processed: 209 average time/residue: 0.5896 time to fit residues: 144.9672 Evaluate side-chains 184 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 433 THR 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 769 GLN 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 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 378 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 916 ILE 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 25 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 236 optimal weight: 0.0010 chunk 118 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.5346 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091464 restraints weight = 32252.946| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.04 r_work: 0.2927 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25785 Z= 0.113 Angle : 0.576 15.947 35151 Z= 0.297 Chirality : 0.047 0.328 4029 Planarity : 0.004 0.054 4458 Dihedral : 6.852 54.698 4360 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.74 % Allowed : 8.87 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.14), residues: 3081 helix: 1.65 (0.21), residues: 681 sheet: 1.04 (0.19), residues: 699 loop : -1.40 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.018 0.001 TYR B1049 PHE 0.012 0.001 PHE C 325 TRP 0.017 0.001 TRP A 868 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00242 (25698) covalent geometry : angle 0.54989 (34935) SS BOND : bond 0.00754 ( 45) SS BOND : angle 2.36541 ( 90) hydrogen bonds : bond 0.05242 ( 1011) hydrogen bonds : angle 5.06701 ( 2937) link_NAG-ASN : bond 0.00465 ( 42) link_NAG-ASN : angle 2.14878 ( 126) *********************** 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 213 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.053 Fit side-chains REVERT: A 151 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5496 (mpt) REVERT: A 426 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7881 (ttm-80) REVERT: A 709 MET cc_start: 0.9398 (mtp) cc_final: 0.9085 (mtp) REVERT: B 130 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6307 (p90) REVERT: B 267 ASP cc_start: 0.8440 (m-30) cc_final: 0.8152 (m-30) REVERT: B 518 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8121 (t0) REVERT: B 1107 ASN cc_start: 0.8809 (p0) cc_final: 0.8512 (p0) REVERT: C 130 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.5295 (p90) REVERT: C 137 PHE cc_start: 0.8244 (p90) cc_final: 0.8040 (p90) REVERT: C 322 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7742 (tm) outliers start: 47 outliers final: 21 residues processed: 200 average time/residue: 0.6407 time to fit residues: 150.0961 Evaluate side-chains 178 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET 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 705 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR 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 518 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER 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 322 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 792 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 224 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 299 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 295 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.118685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.091583 restraints weight = 32285.542| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.06 r_work: 0.2925 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1866 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= 0.115 Angle : 0.589 17.943 35151 Z= 0.298 Chirality : 0.047 0.318 4029 Planarity : 0.004 0.053 4458 Dihedral : 6.470 50.758 4360 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.89 % Allowed : 9.43 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.14), residues: 3081 helix: 1.82 (0.21), residues: 678 sheet: 0.98 (0.19), residues: 738 loop : -1.39 (0.13), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.019 0.001 TYR B1049 PHE 0.009 0.001 PHE B 870 TRP 0.018 0.001 TRP A 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00254 (25698) covalent geometry : angle 0.56108 (34935) SS BOND : bond 0.00664 ( 45) SS BOND : angle 2.70338 ( 90) hydrogen bonds : bond 0.05140 ( 1011) hydrogen bonds : angle 4.98145 ( 2937) link_NAG-ASN : bond 0.00430 ( 42) link_NAG-ASN : angle 2.02796 ( 126) *********************** 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 215 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 1.336 Fit side-chains REVERT: A 151 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5510 (mpt) REVERT: A 426 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7905 (ttm-80) REVERT: A 709 MET cc_start: 0.9389 (mtp) cc_final: 0.9147 (mtp) REVERT: A 825 ASP cc_start: 0.6314 (m-30) cc_final: 0.6086 (t0) REVERT: A 851 MET cc_start: 0.8985 (mtt) cc_final: 0.8639 (mtt) REVERT: B 130 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6902 (p90) REVERT: B 267 ASP cc_start: 0.8438 (m-30) cc_final: 0.8185 (m-30) REVERT: B 796 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7870 (mmtm) REVERT: B 1107 ASN cc_start: 0.8817 (p0) cc_final: 0.8492 (p0) REVERT: C 130 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.5231 (p90) REVERT: C 137 PHE cc_start: 0.8302 (p90) cc_final: 0.8094 (p90) REVERT: C 322 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7944 (tm) REVERT: C 593 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8169 (mm-30) REVERT: C 851 MET cc_start: 0.9063 (mtt) cc_final: 0.8737 (mtt) outliers start: 51 outliers final: 28 residues processed: 200 average time/residue: 0.6513 time to fit residues: 152.7250 Evaluate side-chains 192 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 ASN 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 705 THR Chi-restraints excluded: chain A residue 795 THR 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 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 810 LEU 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 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 679 MET Chi-restraints excluded: chain C residue 708 VAL 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 288 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 0.0020 chunk 266 optimal weight: 0.0770 chunk 252 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7948 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.118484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.091357 restraints weight = 32475.015| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.11 r_work: 0.2923 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1970 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= 0.117 Angle : 0.577 17.050 35151 Z= 0.293 Chirality : 0.047 0.313 4029 Planarity : 0.004 0.052 4458 Dihedral : 6.177 48.662 4360 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.60 % Allowed : 9.06 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.14), residues: 3081 helix: 1.89 (0.21), residues: 678 sheet: 1.04 (0.19), residues: 708 loop : -1.36 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.019 0.001 TYR B1049 PHE 0.010 0.001 PHE B 870 TRP 0.022 0.001 TRP A 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00261 (25698) covalent geometry : angle 0.55175 (34935) SS BOND : bond 0.00555 ( 45) SS BOND : angle 2.52427 ( 90) hydrogen bonds : bond 0.05179 ( 1011) hydrogen bonds : angle 4.93147 ( 2937) link_NAG-ASN : bond 0.00419 ( 42) link_NAG-ASN : angle 1.95765 ( 126) *********************** 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 : 1.241 Fit side-chains REVERT: A 151 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5527 (mpt) REVERT: A 426 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.7907 (ttm-80) REVERT: A 709 MET cc_start: 0.9361 (mtp) cc_final: 0.9079 (mtp) REVERT: A 816 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7961 (tpp) REVERT: A 851 MET cc_start: 0.8967 (mtt) cc_final: 0.8578 (mtt) REVERT: B 130 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7263 (p90) REVERT: B 792 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8017 (tt) REVERT: B 796 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7921 (mmtm) REVERT: B 1107 ASN cc_start: 0.8828 (p0) cc_final: 0.8485 (p0) REVERT: C 130 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.5588 (p90) REVERT: C 137 PHE cc_start: 0.8355 (p90) cc_final: 0.8146 (p90) REVERT: C 322 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8049 (tm) REVERT: C 593 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8167 (mm-30) REVERT: C 851 MET cc_start: 0.9078 (mtt) cc_final: 0.8729 (mtt) outliers start: 70 outliers final: 34 residues processed: 207 average time/residue: 0.5975 time to fit residues: 145.4572 Evaluate side-chains 193 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 720 CYS 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 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 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 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 322 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 626 ASN 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 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 152 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.115662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088482 restraints weight = 32355.525| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.07 r_work: 0.2879 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25785 Z= 0.181 Angle : 0.658 19.627 35151 Z= 0.334 Chirality : 0.050 0.377 4029 Planarity : 0.004 0.051 4458 Dihedral : 6.467 53.847 4358 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.41 % Allowed : 9.54 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.14), residues: 3081 helix: 1.49 (0.20), residues: 702 sheet: 1.09 (0.20), residues: 672 loop : -1.43 (0.12), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 306 TYR 0.021 0.002 TYR B1049 PHE 0.015 0.002 PHE A 870 TRP 0.026 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00434 (25698) covalent geometry : angle 0.63074 (34935) SS BOND : bond 0.00782 ( 45) SS BOND : angle 2.76799 ( 90) hydrogen bonds : bond 0.06529 ( 1011) hydrogen bonds : angle 5.15474 ( 2937) link_NAG-ASN : bond 0.00379 ( 42) link_NAG-ASN : angle 2.23427 ( 126) *********************** 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 229 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 0.990 Fit side-chains REVERT: A 130 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7053 (p90) REVERT: A 151 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5497 (mpt) REVERT: A 426 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7919 (ttm-80) REVERT: A 709 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9079 (mtp) REVERT: A 816 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7894 (tpp) REVERT: B 130 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7444 (p90) REVERT: B 796 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7941 (mmtm) REVERT: B 816 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8491 (ttp) REVERT: B 825 ASP cc_start: 0.6419 (m-30) cc_final: 0.6150 (t0) REVERT: B 1107 ASN cc_start: 0.8896 (p0) cc_final: 0.8592 (p0) REVERT: C 130 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6879 (p90) REVERT: C 593 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8162 (mm-30) REVERT: C 851 MET cc_start: 0.9142 (mtt) cc_final: 0.8806 (mtt) outliers start: 65 outliers final: 39 residues processed: 206 average time/residue: 0.6208 time to fit residues: 149.4572 Evaluate side-chains 208 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 151 MET 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 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 827 ASN Chi-restraints excluded: chain A residue 916 ILE 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 433 THR 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 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 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 1108 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 205 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 244 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.116699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089488 restraints weight = 32419.257| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.10 r_work: 0.2885 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2063 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= 0.144 Angle : 0.620 19.497 35151 Z= 0.314 Chirality : 0.048 0.351 4029 Planarity : 0.004 0.051 4458 Dihedral : 6.344 52.494 4358 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 9.76 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.14), residues: 3081 helix: 1.60 (0.20), residues: 699 sheet: 1.05 (0.20), residues: 672 loop : -1.45 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 306 TYR 0.019 0.001 TYR B1049 PHE 0.012 0.001 PHE B 870 TRP 0.031 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00335 (25698) covalent geometry : angle 0.59301 (34935) SS BOND : bond 0.00644 ( 45) SS BOND : angle 2.68327 ( 90) hydrogen bonds : bond 0.05853 ( 1011) hydrogen bonds : angle 5.07333 ( 2937) link_NAG-ASN : bond 0.00405 ( 42) link_NAG-ASN : angle 2.12221 ( 126) *********************** 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: 62 poor density : 159 time to evaluate : 0.940 Fit side-chains REVERT: A 93 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: A 151 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5465 (mpt) REVERT: A 426 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7923 (ttm-80) REVERT: A 709 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9135 (mtp) REVERT: A 851 MET cc_start: 0.8997 (mtt) cc_final: 0.8595 (mtt) REVERT: A 1020 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8800 (mmtm) REVERT: B 130 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7482 (p90) REVERT: B 796 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8031 (mmtm) REVERT: B 816 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: B 825 ASP cc_start: 0.6480 (m-30) cc_final: 0.6211 (t0) REVERT: B 1107 ASN cc_start: 0.8889 (p0) cc_final: 0.8573 (p0) REVERT: C 130 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7152 (p90) REVERT: C 593 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8197 (mm-30) REVERT: C 851 MET cc_start: 0.9107 (mtt) cc_final: 0.8752 (mtt) outliers start: 62 outliers final: 41 residues processed: 201 average time/residue: 0.6094 time to fit residues: 143.3151 Evaluate side-chains 207 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 260 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 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 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1020 LYS 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 162 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 626 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.114626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087149 restraints weight = 32518.284| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.07 r_work: 0.2876 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25785 Z= 0.185 Angle : 0.673 20.264 35151 Z= 0.341 Chirality : 0.051 0.399 4029 Planarity : 0.004 0.050 4458 Dihedral : 6.558 54.947 4358 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.23 % Allowed : 10.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3081 helix: 1.46 (0.20), residues: 699 sheet: 1.14 (0.20), residues: 642 loop : -1.46 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 306 TYR 0.021 0.002 TYR B1049 PHE 0.015 0.002 PHE A 870 TRP 0.037 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00446 (25698) covalent geometry : angle 0.64454 (34935) SS BOND : bond 0.00803 ( 45) SS BOND : angle 2.87998 ( 90) hydrogen bonds : bond 0.06654 ( 1011) hydrogen bonds : angle 5.20974 ( 2937) link_NAG-ASN : bond 0.00382 ( 42) link_NAG-ASN : angle 2.30294 ( 126) *********************** 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 224 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 1.067 Fit side-chains REVERT: A 93 GLU cc_start: 0.8112 (tp30) cc_final: 0.7834 (mm-30) REVERT: A 151 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5500 (mpt) REVERT: A 426 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7907 (ttm-80) REVERT: A 709 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9098 (mtp) REVERT: A 1020 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8797 (mmtm) REVERT: B 130 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7336 (p90) REVERT: B 796 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8061 (mmtm) REVERT: B 816 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8478 (ttp) REVERT: B 825 ASP cc_start: 0.6610 (m-30) cc_final: 0.6371 (t0) REVERT: B 1107 ASN cc_start: 0.8926 (p0) cc_final: 0.8593 (p0) REVERT: C 130 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.6802 (p90) REVERT: C 593 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8165 (mm-30) REVERT: C 851 MET cc_start: 0.9140 (mtt) cc_final: 0.8713 (mtt) outliers start: 60 outliers final: 42 residues processed: 208 average time/residue: 0.6324 time to fit residues: 153.6151 Evaluate side-chains 211 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 260 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 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 916 ILE Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1020 LYS 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 433 THR 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 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 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 143 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.117747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.090657 restraints weight = 32253.064| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.01 r_work: 0.2931 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25785 Z= 0.118 Angle : 0.593 17.788 35151 Z= 0.301 Chirality : 0.047 0.322 4029 Planarity : 0.004 0.050 4458 Dihedral : 6.212 49.758 4358 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.63 % Allowed : 10.91 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3081 helix: 1.66 (0.20), residues: 699 sheet: 1.06 (0.19), residues: 672 loop : -1.40 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.019 0.001 TYR C1120 PHE 0.010 0.001 PHE A 137 TRP 0.036 0.002 TRP A 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00264 (25698) covalent geometry : angle 0.56721 (34935) SS BOND : bond 0.00545 ( 45) SS BOND : angle 2.58858 ( 90) hydrogen bonds : bond 0.05274 ( 1011) hydrogen bonds : angle 4.99639 ( 2937) link_NAG-ASN : bond 0.00422 ( 42) link_NAG-ASN : angle 2.01977 ( 126) ********************** 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 205 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.008 Fit side-chains REVERT: A 93 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: A 151 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5399 (mpt) REVERT: A 426 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7896 (ttm-80) REVERT: A 685 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 709 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9123 (mtp) REVERT: A 851 MET cc_start: 0.8980 (mtt) cc_final: 0.8569 (mtt) REVERT: A 1020 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8770 (mmtm) REVERT: B 130 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7549 (p90) REVERT: B 796 LYS cc_start: 0.8327 (mmmt) cc_final: 0.8088 (mmtm) REVERT: B 825 ASP cc_start: 0.6529 (m-30) cc_final: 0.6313 (t0) REVERT: B 1107 ASN cc_start: 0.8900 (p0) cc_final: 0.8567 (p0) REVERT: C 130 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7223 (p90) REVERT: C 708 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8832 (t) REVERT: C 851 MET cc_start: 0.9053 (mtt) cc_final: 0.8680 (mtt) outliers start: 44 outliers final: 27 residues processed: 194 average time/residue: 0.6083 time to fit residues: 138.7915 Evaluate side-chains 191 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 260 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 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 795 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1020 LYS 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 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 792 LEU Chi-restraints excluded: chain B residue 795 THR 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 306 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3478 r_free = 0.3478 target = 0.117245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.090101 restraints weight = 32327.198| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.10 r_work: 0.2895 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2167 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= 0.134 Angle : 0.623 18.281 35151 Z= 0.315 Chirality : 0.048 0.329 4029 Planarity : 0.004 0.050 4458 Dihedral : 6.228 51.254 4358 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.71 % Allowed : 10.84 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.14), residues: 3081 helix: 1.66 (0.20), residues: 699 sheet: 1.07 (0.19), residues: 672 loop : -1.38 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.021 0.001 TYR B1120 PHE 0.012 0.001 PHE A 137 TRP 0.042 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00309 (25698) covalent geometry : angle 0.59538 (34935) SS BOND : bond 0.00666 ( 45) SS BOND : angle 2.83833 ( 90) hydrogen bonds : bond 0.05574 ( 1011) hydrogen bonds : angle 5.02156 ( 2937) link_NAG-ASN : bond 0.00399 ( 42) link_NAG-ASN : angle 2.03924 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8774.23 seconds wall clock time: 150 minutes 16.04 seconds (9016.04 seconds total)