Starting phenix.real_space_refine on Sun Jul 5 04:18:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_34417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_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_34417/07_2026/8h0x_34417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_34417.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_34417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_34417.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_34417.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h0x_34417/07_2026/8h0x_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 chiralities: 14 Time building chain proxies: 4.48, per 1000 atoms: 0.18 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: 1.86 Conformation dependent library (CDL) restraints added in 920.1 milliseconds 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: 0.78 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: 5.91 Time building geometry restraints manager: 2.49 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: 13820 17.44 - 34.89: 837 34.89 - 52.33: 182 52.33 - 69.78: 35 69.78 - 87.22: 39 Dihedral angle restraints: 14913 sinusoidal: 5838 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 14910 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.220 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 12.741 87.220 8946 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 are 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/Z covalent geometry : bond 0.00788 / 0.38 (25698) covalent geometry : angle 0.92778 / 0.50 (34935) SS BOND : bond 0.00987 / 0.57 ( 45) SS BOND : angle 2.29216 / 1.80 ( 90) hydrogen bonds : bond 0.14447 / 9.54 ( 1011) hydrogen bonds : angle 6.20508 / 4.34 ( 2937) link_NAG-ASN : bond 0.00566 / 0.39 ( 42) link_NAG-ASN : angle 3.92611 / 2.69 ( 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 : 0.989 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: 0.6587 time to fit residues: 205.9428 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 : 0.892 ------------------------------------------------------------------------------- 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... 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 = 0.3504 r_free = 0.3504 target = 0.119110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.091544 restraints weight = 32291.686| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.18 r_work: 0.2964 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1167 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= 0.133 Angle : 0.598 14.257 35151 Z= 0.311 Chirality : 0.048 0.353 4029 Planarity : 0.005 0.063 4458 Dihedral : 6.153 67.640 3443 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.34 % Allowed : 6.24 % Favored : 92.43 % 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 are not related in a simple way. whole: -0.35 (0.14), residues: 3081 helix: 1.29 (0.20), residues: 681 sheet: 1.09 (0.19), residues: 687 loop : -1.52 (0.12), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 544 TYR 0.019 0.001 TYR A1120 PHE 0.013 0.001 PHE C 334 TRP 0.017 0.001 TRP A 868 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25698) covalent geometry : angle 0.57456 / 0.30 (34935) SS BOND : bond 0.00592 / 0.36 ( 45) SS BOND : angle 1.86525 / 1.25 ( 90) hydrogen bonds : bond 0.05761 / 3.71 ( 1011) hydrogen bonds : angle 5.20290 / 3.60 ( 2937) link_NAG-ASN : bond 0.00477 / 0.35 ( 42) link_NAG-ASN : angle 2.43003 / 1.67 ( 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 218 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.952 Fit side-chains REVERT: A 544 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8324 (ptp90) REVERT: B 518 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8188 (t0) REVERT: B 769 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: C 130 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.5347 (p90) REVERT: C 151 MET cc_start: 0.7388 (mmt) cc_final: 0.7051 (mmt) outliers start: 36 outliers final: 14 residues processed: 203 average time/residue: 0.5293 time to fit residues: 125.8860 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 : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain 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 768 LYS Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain B residue 823 LEU 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: 3.9990 chunk 303 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 101 optimal weight: 0.1980 chunk 247 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3479 r_free = 0.3479 target = 0.117287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.089734 restraints weight = 32300.902| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.12 r_work: 0.2910 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25785 Z= 0.151 Angle : 0.619 15.534 35151 Z= 0.320 Chirality : 0.049 0.363 4029 Planarity : 0.004 0.056 4458 Dihedral : 5.911 60.285 3430 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.86 % Allowed : 7.46 % Favored : 90.68 % 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 are not related in a simple way. whole: -0.23 (0.14), residues: 3081 helix: 1.51 (0.21), residues: 681 sheet: 1.05 (0.19), residues: 699 loop : -1.46 (0.12), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.020 0.002 TYR B1049 PHE 0.014 0.001 PHE B 870 TRP 0.021 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25698) covalent geometry : angle 0.59476 / 0.31 (34935) SS BOND : bond 0.00634 / 0.40 ( 45) SS BOND : angle 2.23963 / 1.66 ( 90) hydrogen bonds : bond 0.06145 / 3.98 ( 1011) hydrogen bonds : angle 5.17401 / 3.60 ( 2937) link_NAG-ASN : bond 0.00418 / 0.31 ( 42) link_NAG-ASN : angle 2.31078 / 1.58 ( 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 218 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 1.024 Fit side-chains REVERT: A 709 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.9171 (mtp) REVERT: B 267 ASP cc_start: 0.8435 (m-30) cc_final: 0.8182 (m-30) REVERT: B 296 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: B 518 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8258 (t0) REVERT: B 768 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7905 (mmtt) REVERT: B 816 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8462 (ttp) REVERT: C 130 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.5289 (p90) REVERT: C 151 MET cc_start: 0.7302 (mmt) cc_final: 0.7051 (mmt) outliers start: 50 outliers final: 23 residues processed: 200 average time/residue: 0.5178 time to fit residues: 121.8411 Evaluate side-chains 181 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 236 optimal weight: 0.0070 chunk 118 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 196 optimal weight: 0.0570 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3535 r_free = 0.3535 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093620 restraints weight = 32254.847| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.09 r_work: 0.2994 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25785 Z= 0.096 Angle : 0.532 11.636 35151 Z= 0.275 Chirality : 0.045 0.288 4029 Planarity : 0.004 0.054 4458 Dihedral : 5.431 47.856 3430 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.37 % Allowed : 8.91 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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 are not related in a simple way. whole: 0.02 (0.14), residues: 3081 helix: 2.05 (0.21), residues: 654 sheet: 1.03 (0.19), residues: 744 loop : -1.38 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 544 TYR 0.020 0.001 TYR B1120 PHE 0.012 0.001 PHE C 325 TRP 0.016 0.001 TRP A 868 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (25698) covalent geometry : angle 0.50790 / 0.27 (34935) SS BOND : bond 0.00631 / 0.37 ( 45) SS BOND : angle 2.20441 / 1.68 ( 90) hydrogen bonds : bond 0.04386 / 2.81 ( 1011) hydrogen bonds : angle 4.89612 / 3.40 ( 2937) link_NAG-ASN : bond 0.00466 / 0.33 ( 42) link_NAG-ASN : angle 1.97058 / 1.34 ( 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 207 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.820 Fit side-chains REVERT: A 426 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8636 (ttt180) REVERT: A 709 MET cc_start: 0.9369 (mtp) cc_final: 0.9160 (mtp) REVERT: A 816 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: B 130 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.5525 (p90) REVERT: B 267 ASP cc_start: 0.8356 (m-30) cc_final: 0.8152 (m-30) REVERT: B 768 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7823 (mmtt) REVERT: B 884 MET cc_start: 0.9203 (tpt) cc_final: 0.8840 (tpt) REVERT: C 130 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.5148 (p90) REVERT: C 162 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: C 322 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7367 (tm) REVERT: C 327 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: C 593 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8206 (mt-10) outliers start: 37 outliers final: 16 residues processed: 196 average time/residue: 0.5583 time to fit residues: 127.6143 Evaluate side-chains 172 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 705 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 768 LYS 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 322 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 792 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: 4.9990 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 299 optimal weight: 3.9990 chunk 263 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3507 r_free = 0.3507 target = 0.119374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.092454 restraints weight = 32236.052| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.05 r_work: 0.2946 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1820 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= 0.119 Angle : 0.587 17.212 35151 Z= 0.297 Chirality : 0.047 0.311 4029 Planarity : 0.004 0.053 4458 Dihedral : 5.437 48.294 3430 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.93 % Allowed : 9.24 % Favored : 88.83 % 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 are not related in a simple way. whole: 0.03 (0.14), residues: 3081 helix: 1.90 (0.21), residues: 678 sheet: 1.02 (0.19), residues: 738 loop : -1.33 (0.13), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 544 TYR 0.019 0.001 TYR B1049 PHE 0.010 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/Z covalent geometry : bond 0.00268 / 0.12 (25698) covalent geometry : angle 0.55990 / 0.29 (34935) SS BOND : bond 0.00594 / 0.39 ( 45) SS BOND : angle 2.72669 / 1.91 ( 90) hydrogen bonds : bond 0.05095 / 3.29 ( 1011) hydrogen bonds : angle 4.91343 / 3.41 ( 2937) link_NAG-ASN : bond 0.00394 / 0.29 ( 42) link_NAG-ASN : angle 1.94554 / 1.33 ( 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 206 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.970 Fit side-chains REVERT: A 151 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5447 (mpt) REVERT: A 426 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8651 (ttt180) REVERT: A 708 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 709 MET cc_start: 0.9376 (mtp) cc_final: 0.9166 (mtp) REVERT: A 816 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8008 (tpp) REVERT: A 851 MET cc_start: 0.8973 (mtt) cc_final: 0.8595 (mtt) REVERT: B 130 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6319 (p90) REVERT: B 796 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7800 (mmtm) REVERT: C 130 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.5232 (p90) REVERT: C 162 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: C 327 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8092 (mp0) outliers start: 52 outliers final: 27 residues processed: 192 average time/residue: 0.5018 time to fit residues: 113.5768 Evaluate side-chains 182 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain A residue 323 CYS 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 708 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 966 LEU 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 966 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 327 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 792 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: 2.9990 chunk 266 optimal weight: 0.0270 chunk 252 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3481 r_free = 0.3481 target = 0.117449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.090248 restraints weight = 32449.294| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.09 r_work: 0.2900 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1900 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= 0.146 Angle : 0.617 17.538 35151 Z= 0.313 Chirality : 0.048 0.335 4029 Planarity : 0.004 0.052 4458 Dihedral : 5.593 52.206 3430 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.56 % Allowed : 9.17 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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 are not related in a simple way. whole: -0.02 (0.14), residues: 3081 helix: 1.82 (0.21), residues: 681 sheet: 1.08 (0.19), residues: 717 loop : -1.37 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 544 TYR 0.021 0.001 TYR B1120 PHE 0.013 0.001 PHE B 870 TRP 0.022 0.001 TRP A 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (25698) covalent geometry : angle 0.59070 / 0.30 (34935) SS BOND : bond 0.00676 / 0.44 ( 45) SS BOND : angle 2.68984 / 1.91 ( 90) hydrogen bonds : bond 0.05848 / 3.77 ( 1011) hydrogen bonds : angle 5.02680 / 3.49 ( 2937) link_NAG-ASN : bond 0.00373 / 0.27 ( 42) link_NAG-ASN : angle 2.04518 / 1.39 ( 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 227 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 158 time to evaluate : 0.945 Fit side-chains REVERT: A 130 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7156 (p90) REVERT: A 151 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5394 (mpt) REVERT: A 306 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7766 (ptp90) REVERT: A 426 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7944 (ttm-80) REVERT: A 708 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8908 (m) REVERT: A 709 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9077 (mtp) REVERT: A 851 MET cc_start: 0.9016 (mtt) cc_final: 0.8635 (mtt) REVERT: B 130 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7391 (p90) REVERT: B 708 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8870 (m) REVERT: B 792 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 796 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7887 (mmtm) REVERT: B 1107 ASN cc_start: 0.8825 (p0) cc_final: 0.8491 (p0) REVERT: C 32 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: C 130 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.5628 (p90) REVERT: C 327 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: C 593 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8176 (mm-30) REVERT: C 966 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8003 (mp) outliers start: 69 outliers final: 34 residues processed: 206 average time/residue: 0.5382 time to fit residues: 131.0877 Evaluate side-chains 201 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 152 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 246 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3486 r_free = 0.3486 target = 0.117800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.090691 restraints weight = 32284.827| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.10 r_work: 0.2906 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25785 Z= 0.130 Angle : 0.591 16.733 35151 Z= 0.300 Chirality : 0.047 0.326 4029 Planarity : 0.004 0.051 4458 Dihedral : 5.456 50.295 3428 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 9.69 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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 are not related in a simple way. whole: -0.01 (0.14), residues: 3081 helix: 1.84 (0.21), residues: 681 sheet: 1.14 (0.19), residues: 687 loop : -1.34 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 544 TYR 0.018 0.001 TYR B1049 PHE 0.011 0.001 PHE B 870 TRP 0.024 0.001 TRP A 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25698) covalent geometry : angle 0.56636 / 0.29 (34935) SS BOND : bond 0.00592 / 0.39 ( 45) SS BOND : angle 2.49031 / 1.76 ( 90) hydrogen bonds : bond 0.05470 / 3.52 ( 1011) hydrogen bonds : angle 4.97045 / 3.45 ( 2937) link_NAG-ASN : bond 0.00386 / 0.28 ( 42) link_NAG-ASN : angle 1.98356 / 1.35 ( 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 217 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.984 Fit side-chains REVERT: A 107 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7678 (mtm) REVERT: A 306 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7791 (ptp90) REVERT: A 426 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7962 (ttm-80) REVERT: A 708 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8905 (m) REVERT: B 130 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7516 (p90) REVERT: B 792 LEU cc_start: 0.8326 (tp) cc_final: 0.8054 (tt) REVERT: B 796 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7902 (mmtm) REVERT: B 1107 ASN cc_start: 0.8842 (p0) cc_final: 0.8484 (p0) REVERT: C 130 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.5601 (p90) REVERT: C 327 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: C 593 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8200 (mm-30) REVERT: C 708 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8849 (m) REVERT: C 966 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8066 (mp) outliers start: 59 outliers final: 33 residues processed: 202 average time/residue: 0.5455 time to fit residues: 129.4837 Evaluate side-chains 196 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 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 966 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 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 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 327 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 708 VAL 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: 10.0000 chunk 105 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.089465 restraints weight = 32516.014| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.07 r_work: 0.2896 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25785 Z= 0.159 Angle : 0.637 20.167 35151 Z= 0.321 Chirality : 0.049 0.346 4029 Planarity : 0.004 0.051 4458 Dihedral : 5.623 53.364 3428 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.23 % Allowed : 9.95 % Favored : 87.82 % 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 are not related in a simple way. whole: -0.16 (0.14), residues: 3081 helix: 1.62 (0.20), residues: 699 sheet: 1.08 (0.20), residues: 672 loop : -1.43 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1021 TYR 0.021 0.002 TYR B1120 PHE 0.014 0.001 PHE B 870 TRP 0.030 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (25698) covalent geometry : angle 0.61070 / 0.31 (34935) SS BOND : bond 0.00701 / 0.46 ( 45) SS BOND : angle 2.71135 / 1.90 ( 90) hydrogen bonds : bond 0.06115 / 3.95 ( 1011) hydrogen bonds : angle 5.08461 / 3.53 ( 2937) link_NAG-ASN : bond 0.00361 / 0.26 ( 42) link_NAG-ASN : angle 2.10045 / 1.42 ( 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 219 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.833 Fit side-chains REVERT: A 130 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7240 (p90) REVERT: A 426 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7929 (ttm-80) REVERT: A 708 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8907 (m) REVERT: A 709 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9082 (mtp) REVERT: A 851 MET cc_start: 0.9014 (mtt) cc_final: 0.8612 (mtt) REVERT: B 130 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7450 (p90) REVERT: B 792 LEU cc_start: 0.8349 (tp) cc_final: 0.8065 (tt) REVERT: B 796 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8026 (mmtm) REVERT: B 816 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: B 825 ASP cc_start: 0.6391 (m-30) cc_final: 0.6138 (t0) REVERT: B 1107 ASN cc_start: 0.8902 (p0) cc_final: 0.8583 (p0) REVERT: C 130 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7009 (p90) REVERT: C 593 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8156 (mm-30) REVERT: C 966 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8219 (mp) outliers start: 60 outliers final: 35 residues processed: 204 average time/residue: 0.5361 time to fit residues: 128.9543 Evaluate side-chains 201 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1108 CYS 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 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 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 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: 5.9990 chunk 293 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3460 r_free = 0.3460 target = 0.115829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.088884 restraints weight = 32490.684| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.10 r_work: 0.2881 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25785 Z= 0.169 Angle : 0.652 19.270 35151 Z= 0.329 Chirality : 0.049 0.361 4029 Planarity : 0.004 0.050 4458 Dihedral : 5.709 53.911 3428 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.93 % Allowed : 10.54 % Favored : 87.53 % 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 are not related in a simple way. whole: -0.17 (0.14), residues: 3081 helix: 1.55 (0.20), residues: 699 sheet: 1.18 (0.20), residues: 642 loop : -1.41 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1021 TYR 0.020 0.002 TYR B1049 PHE 0.015 0.001 PHE A 870 TRP 0.037 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (25698) covalent geometry : angle 0.62511 / 0.32 (34935) SS BOND : bond 0.00736 / 0.48 ( 45) SS BOND : angle 2.75964 / 1.96 ( 90) hydrogen bonds : bond 0.06322 / 4.08 ( 1011) hydrogen bonds : angle 5.13967 / 3.57 ( 2937) link_NAG-ASN : bond 0.00369 / 0.27 ( 42) link_NAG-ASN : angle 2.19802 / 1.49 ( 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 210 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.904 Fit side-chains REVERT: A 93 GLU cc_start: 0.8107 (tp30) cc_final: 0.7786 (mm-30) REVERT: A 151 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6323 (mpp) REVERT: A 426 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7936 (ttm-80) REVERT: A 708 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8846 (t) REVERT: A 709 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9090 (mtp) REVERT: A 851 MET cc_start: 0.9022 (mtt) cc_final: 0.8620 (mtt) REVERT: B 130 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7272 (p90) REVERT: B 792 LEU cc_start: 0.8358 (tp) cc_final: 0.8055 (tt) REVERT: B 796 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8106 (mmtm) REVERT: B 816 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: B 825 ASP cc_start: 0.6552 (m-30) cc_final: 0.6283 (t0) REVERT: B 1107 ASN cc_start: 0.8910 (p0) cc_final: 0.8565 (p0) REVERT: C 130 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.6964 (p90) REVERT: C 593 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8160 (mm-30) REVERT: C 966 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8346 (mp) outliers start: 52 outliers final: 36 residues processed: 198 average time/residue: 0.5254 time to fit residues: 122.7559 Evaluate side-chains 200 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 378 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1108 CYS 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 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 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 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 143 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 chunk 159 optimal weight: 0.0000 chunk 138 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091291 restraints weight = 32267.239| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.07 r_work: 0.2916 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25785 Z= 0.114 Angle : 0.581 17.672 35151 Z= 0.294 Chirality : 0.047 0.313 4029 Planarity : 0.004 0.050 4458 Dihedral : 5.416 49.312 3428 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.52 % Allowed : 10.95 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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 are not related in a simple way. whole: -0.08 (0.14), residues: 3081 helix: 1.71 (0.20), residues: 699 sheet: 1.08 (0.19), residues: 672 loop : -1.37 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 544 TYR 0.020 0.001 TYR B1120 PHE 0.010 0.001 PHE A 137 TRP 0.035 0.001 TRP A 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (25698) covalent geometry : angle 0.55679 / 0.29 (34935) SS BOND : bond 0.00538 / 0.36 ( 45) SS BOND : angle 2.45820 / 1.74 ( 90) hydrogen bonds : bond 0.05190 / 3.34 ( 1011) hydrogen bonds : angle 4.95912 / 3.45 ( 2937) link_NAG-ASN : bond 0.00400 / 0.29 ( 42) link_NAG-ASN : angle 1.95212 / 1.33 ( 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 203 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.757 Fit side-chains REVERT: A 93 GLU cc_start: 0.8006 (tp30) cc_final: 0.7716 (mm-30) REVERT: A 151 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6212 (mpp) REVERT: A 426 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7948 (ttm-80) REVERT: A 685 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7148 (p) REVERT: A 709 MET cc_start: 0.9398 (mtp) cc_final: 0.9183 (mtp) REVERT: A 851 MET cc_start: 0.9003 (mtt) cc_final: 0.8599 (mtt) REVERT: B 130 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7541 (p90) REVERT: B 792 LEU cc_start: 0.8363 (tp) cc_final: 0.8057 (tt) REVERT: B 796 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8096 (mmtm) REVERT: B 825 ASP cc_start: 0.6563 (m-30) cc_final: 0.6291 (t0) REVERT: B 1107 ASN cc_start: 0.8894 (p0) cc_final: 0.8555 (p0) REVERT: C 130 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7276 (p90) REVERT: C 593 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8204 (mm-30) REVERT: C 708 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8822 (t) REVERT: C 966 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8203 (mp) outliers start: 41 outliers final: 30 residues processed: 196 average time/residue: 0.5357 time to fit residues: 123.6580 Evaluate side-chains 193 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 628 VAL Chi-restraints excluded: chain A residue 685 SER 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 966 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1108 CYS 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 515 LEU 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 795 THR 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 306 ARG Chi-restraints excluded: chain C residue 378 CYS 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: 1.9990 chunk 64 optimal weight: 0.5980 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090189 restraints weight = 32348.111| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.05 r_work: 0.2893 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25785 Z= 0.138 Angle : 0.610 18.490 35151 Z= 0.309 Chirality : 0.048 0.328 4029 Planarity : 0.004 0.050 4458 Dihedral : 5.486 51.497 3428 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 11.02 % Favored : 87.34 % 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 are not related in a simple way. whole: -0.09 (0.14), residues: 3081 helix: 1.70 (0.20), residues: 699 sheet: 1.08 (0.19), residues: 672 loop : -1.38 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1021 TYR 0.019 0.001 TYR B1049 PHE 0.012 0.001 PHE A 870 TRP 0.041 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (25698) covalent geometry : angle 0.58505 / 0.30 (34935) SS BOND : bond 0.00613 / 0.40 ( 45) SS BOND : angle 2.58156 / 1.82 ( 90) hydrogen bonds : bond 0.05689 / 3.67 ( 1011) hydrogen bonds : angle 5.01674 / 3.49 ( 2937) link_NAG-ASN : bond 0.00377 / 0.27 ( 42) link_NAG-ASN : angle 2.00521 / 1.36 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7809.43 seconds wall clock time: 133 minutes 37.96 seconds (8017.96 seconds total)