Starting phenix.real_space_refine on Sun Jul 5 06:14:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhh_31994/07_2026/7vhh_31994.map" } resolution = 3.8 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= 0.002 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 117 5.16 5 C 16420 2.51 5 N 4223 2.21 5 O 5035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 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: 25795 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "C" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.19, per 1000 atoms: 0.20 Number of scatterers: 25795 At special positions: 0 Unit cell: (151.94, 153.01, 180.83, 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 117 16.00 O 5035 8.00 N 4223 7.00 C 16420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 282 " " NAG A1204 " - " ASN A 331 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 603 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A1074 " " NAG A1211 " - " ASN A 165 " " NAG A1212 " - " ASN A 234 " " NAG B1201 " - " ASN B 122 " " NAG B1202 " - " ASN B 282 " " NAG B1203 " - " ASN B 331 " " NAG B1204 " - " ASN B 343 " " NAG B1205 " - " ASN B 603 " " NAG B1206 " - " ASN B 616 " " NAG B1207 " - " ASN B 657 " " NAG B1208 " - " ASN B 710 " " NAG B1209 " - " ASN B1074 " " NAG B1210 " - " ASN B 165 " " NAG B1211 " - " ASN B 234 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 282 " " NAG C1204 " - " ASN C 331 " " NAG C1205 " - " ASN C 343 " " NAG C1206 " - " ASN C 603 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG C1210 " - " ASN C1074 " " NAG C1211 " - " ASN C 165 " " NAG C1212 " - " ASN C 234 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B1134 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 24.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.828A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.415A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.769A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.644A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.600A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.258A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.680A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 851 through 857 removed outlier: 3.629A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 857' Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.900A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.121A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.778A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.777A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.511A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.591A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1015 removed outlier: 4.078A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1032 removed outlier: 3.896A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.829A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.416A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.770A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.644A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.600A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.259A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.680A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 851 through 857 removed outlier: 3.629A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 857' Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.901A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.122A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.777A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.778A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.511A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.592A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1015 removed outlier: 4.079A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1032 removed outlier: 3.895A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.828A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.416A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.769A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.645A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.599A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.259A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.679A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 851 through 857 removed outlier: 3.628A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY C 857 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 857' Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.900A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.122A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.777A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.777A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.512A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.592A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1015 removed outlier: 4.078A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.896A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.619A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.559A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.838A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.506A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.691A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.116A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.531A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.634A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.801A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 721 through 723 removed outlier: 7.199A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.902A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 734 through 736 removed outlier: 4.165A pdb=" N SER B 735 " --> pdb=" O ASN B 859 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.620A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.560A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.853A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.506A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.691A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.116A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.532A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.739A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.599A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 721 through 723 removed outlier: 7.199A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 726 through 728 removed outlier: 3.901A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 removed outlier: 4.164A pdb=" N SER A 735 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.620A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.560A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.854A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.507A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.691A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.115A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.532A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.739A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 721 through 723 removed outlier: 7.199A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 726 through 728 removed outlier: 3.902A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 removed outlier: 4.164A pdb=" N SER C 735 " --> pdb=" O ASN C 859 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 1089 through 1090 821 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6046 1.33 - 1.46: 6630 1.46 - 1.58: 13542 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 26365 Sorted by residual: bond pdb=" N ILE C 714 " pdb=" CA ILE C 714 " ideal model delta sigma weight residual 1.454 1.495 -0.040 7.70e-03 1.69e+04 2.71e+01 bond pdb=" N ILE C 716 " pdb=" CA ILE C 716 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.18e+01 bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.15e-02 7.56e+03 1.18e+01 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.15e+01 ... (remaining 26360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 34575 2.15 - 4.31: 1193 4.31 - 6.46: 68 6.46 - 8.61: 13 8.61 - 10.77: 6 Bond angle restraints: 35855 Sorted by residual: angle pdb=" CA ILE C 714 " pdb=" C ILE C 714 " pdb=" O ILE C 714 " ideal model delta sigma weight residual 119.94 116.59 3.35 5.20e-01 3.70e+00 4.15e+01 angle pdb=" N ASN A1098 " pdb=" CA ASN A1098 " pdb=" C ASN A1098 " ideal model delta sigma weight residual 113.16 107.07 6.09 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N ASN C 606 " pdb=" CA ASN C 606 " pdb=" C ASN C 606 " ideal model delta sigma weight residual 113.72 108.27 5.45 1.30e+00 5.92e-01 1.76e+01 angle pdb=" N ASN C1098 " pdb=" CA ASN C1098 " pdb=" C ASN C1098 " ideal model delta sigma weight residual 113.16 108.11 5.05 1.24e+00 6.50e-01 1.66e+01 angle pdb=" N ILE A 716 " pdb=" CA ILE A 716 " pdb=" C ILE A 716 " ideal model delta sigma weight residual 113.10 109.18 3.92 9.70e-01 1.06e+00 1.64e+01 ... (remaining 35850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 13673 17.29 - 34.58: 1277 34.58 - 51.87: 215 51.87 - 69.16: 47 69.16 - 86.45: 25 Dihedral angle restraints: 15237 sinusoidal: 5952 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.55 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.55 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.54 63.54 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 15234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.936: 4224 0.936 - 1.871: 0 1.871 - 2.807: 1 2.807 - 3.743: 0 3.743 - 4.679: 3 Chirality restraints: 4228 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 2.10 -4.50 2.00e-02 2.50e+03 5.07e+04 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.16 -2.24 2.00e-02 2.50e+03 1.26e+04 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-01 2.50e+01 5.47e+02 ... (remaining 4225 not shown) Planarity restraints: 4612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1210 " -0.345 2.00e-02 2.50e+03 2.95e-01 1.08e+03 pdb=" C7 NAG C1210 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C1210 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG C1210 " 0.520 2.00e-02 2.50e+03 pdb=" O7 NAG C1210 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.327 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG N 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.117 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1208 " 0.324 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A1208 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG A1208 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG A1208 " -0.506 2.00e-02 2.50e+03 pdb=" O7 NAG A1208 " 0.157 2.00e-02 2.50e+03 ... (remaining 4609 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 9 2.19 - 2.87: 9984 2.87 - 3.54: 35014 3.54 - 4.22: 57605 4.22 - 4.90: 97220 Nonbonded interactions: 199832 Sorted by model distance: nonbonded pdb=" OG SER C 803 " pdb=" C1 NAG M 1 " model vdw 1.511 3.470 nonbonded pdb=" OG1 THR B1100 " pdb=" C1 NAG F 1 " model vdw 1.522 3.470 nonbonded pdb=" OG1 THR A1100 " pdb=" C1 NAG J 1 " model vdw 1.525 3.470 nonbonded pdb=" ND2 ASN B 709 " pdb=" C1 NAG B1208 " model vdw 1.525 3.550 nonbonded pdb=" OG1 THR C1100 " pdb=" C1 NAG N 1 " model vdw 1.527 3.470 ... (remaining 199827 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 14 through 1211) selection = chain 'B' selection = (chain 'C' and resid 14 through 1211) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.640 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.006 0.069 26466 Z= 0.351 Angle : 0.887 18.451 36116 Z= 0.492 Chirality : 0.141 4.679 4228 Planarity : 0.022 0.295 4565 Dihedral : 13.819 86.454 9135 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.29 % Rotamer: Outliers : 0.83 % Allowed : 1.22 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.14), residues: 3150 helix: -1.40 (0.18), residues: 657 sheet: -1.23 (0.21), residues: 633 loop : -2.39 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 905 TYR 0.013 0.001 TYR C 160 PHE 0.026 0.002 PHE C 157 TRP 0.026 0.002 TRP A 104 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.35 (26365) covalent geometry : angle 0.83296 / 0.48 (35855) SS BOND : bond 0.00604 / 0.48 ( 42) SS BOND : angle 1.28052 / 0.89 ( 84) hydrogen bonds : bond 0.27047 / 17.89 ( 803) hydrogen bonds : angle 9.68601 / 6.69 ( 2172) link_BETA1-4 : bond 0.01283 / 0.69 ( 12) link_BETA1-4 : angle 4.10726 / 3.30 ( 36) link_NAG-ASN : bond 0.01543 / 1.08 ( 47) link_NAG-ASN : angle 4.42753 / 3.35 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: B 153 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.4730 (tpt) REVERT: B 177 MET cc_start: -0.1003 (tpt) cc_final: -0.1237 (tpt) REVERT: B 351 TYR cc_start: 0.5342 (p90) cc_final: 0.4921 (p90) REVERT: B 726 ILE cc_start: 0.9499 (mp) cc_final: 0.9110 (mt) REVERT: A 41 LYS cc_start: 0.6497 (tmtt) cc_final: 0.5929 (mmmm) REVERT: A 118 LEU cc_start: 0.8214 (tp) cc_final: 0.8004 (mt) REVERT: A 133 PHE cc_start: 0.7499 (m-80) cc_final: 0.7060 (m-80) REVERT: A 177 MET cc_start: -0.0698 (tpt) cc_final: -0.1012 (tpt) REVERT: A 726 ILE cc_start: 0.9563 (mp) cc_final: 0.9357 (mt) REVERT: A 1050 MET cc_start: 0.8443 (ptm) cc_final: 0.8027 (ptp) REVERT: C 41 LYS cc_start: 0.5941 (tmtt) cc_final: 0.5385 (mmtt) REVERT: C 133 PHE cc_start: 0.7182 (m-80) cc_final: 0.6929 (m-10) REVERT: C 360 ASN cc_start: 0.8435 (m-40) cc_final: 0.8223 (m-40) REVERT: C 726 ILE cc_start: 0.9576 (mp) cc_final: 0.9235 (mt) outliers start: 23 outliers final: 5 residues processed: 239 average time/residue: 0.1726 time to fit residues: 64.9528 Evaluate side-chains 126 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain A residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 709 ASN A 658 ASN A 895 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083152 restraints weight = 66937.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080832 restraints weight = 55179.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081669 restraints weight = 61567.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082307 restraints weight = 41848.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082585 restraints weight = 37553.136| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26466 Z= 0.188 Angle : 0.805 16.467 36116 Z= 0.383 Chirality : 0.053 0.951 4228 Planarity : 0.005 0.048 4565 Dihedral : 5.669 48.137 3425 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.93 % Allowed : 7.79 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.14), residues: 3150 helix: -0.38 (0.20), residues: 672 sheet: -0.69 (0.21), residues: 624 loop : -2.33 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.015 0.001 TYR A 904 PHE 0.033 0.002 PHE B 133 TRP 0.017 0.001 TRP B 104 HIS 0.005 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (26365) covalent geometry : angle 0.75609 / 0.37 (35855) SS BOND : bond 0.00277 / 0.17 ( 42) SS BOND : angle 2.04467 / 1.40 ( 84) hydrogen bonds : bond 0.06245 / 4.10 ( 803) hydrogen bonds : angle 6.52122 / 4.50 ( 2172) link_BETA1-4 : bond 0.00921 / 0.51 ( 12) link_BETA1-4 : angle 2.93459 / 1.87 ( 36) link_NAG-ASN : bond 0.00815 / 0.51 ( 47) link_NAG-ASN : angle 3.97552 / 2.53 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5543 (tmm) cc_final: 0.4932 (tpt) REVERT: B 177 MET cc_start: -0.0899 (tpt) cc_final: -0.1317 (tpt) REVERT: B 565 PHE cc_start: 0.7992 (m-80) cc_final: 0.7700 (m-10) REVERT: B 592 PHE cc_start: 0.6713 (t80) cc_final: 0.6436 (t80) REVERT: B 726 ILE cc_start: 0.9485 (mp) cc_final: 0.9093 (mt) REVERT: A 41 LYS cc_start: 0.6250 (tmtt) cc_final: 0.5847 (mmmm) REVERT: A 118 LEU cc_start: 0.8563 (tp) cc_final: 0.8193 (mt) REVERT: A 133 PHE cc_start: 0.7451 (m-80) cc_final: 0.7053 (m-80) REVERT: A 177 MET cc_start: -0.1160 (tpt) cc_final: -0.1511 (tpt) REVERT: A 592 PHE cc_start: 0.6385 (p90) cc_final: 0.6177 (p90) REVERT: A 726 ILE cc_start: 0.9566 (mp) cc_final: 0.9359 (mt) REVERT: A 1050 MET cc_start: 0.8543 (ptm) cc_final: 0.8258 (ptp) REVERT: C 360 ASN cc_start: 0.8592 (m-40) cc_final: 0.8357 (m-40) REVERT: C 726 ILE cc_start: 0.9555 (mp) cc_final: 0.9223 (mt) outliers start: 26 outliers final: 14 residues processed: 164 average time/residue: 0.1430 time to fit residues: 39.2360 Evaluate side-chains 127 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 183 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 73 optimal weight: 0.0770 chunk 263 optimal weight: 5.9990 chunk 288 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN B1118 HIS A 134 GLN C 134 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082519 restraints weight = 67010.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081131 restraints weight = 49833.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081993 restraints weight = 57609.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082245 restraints weight = 38848.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082870 restraints weight = 34823.189| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26466 Z= 0.167 Angle : 0.712 13.142 36116 Z= 0.342 Chirality : 0.048 0.394 4228 Planarity : 0.004 0.045 4565 Dihedral : 5.277 36.318 3415 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.72 % Allowed : 10.51 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3150 helix: 0.14 (0.21), residues: 648 sheet: -1.03 (0.20), residues: 645 loop : -2.24 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.017 0.001 TYR A1067 PHE 0.030 0.002 PHE B 157 TRP 0.012 0.001 TRP B 104 HIS 0.005 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (26365) covalent geometry : angle 0.67461 / 0.33 (35855) SS BOND : bond 0.00405 / 0.24 ( 42) SS BOND : angle 2.00313 / 1.29 ( 84) hydrogen bonds : bond 0.04831 / 3.20 ( 803) hydrogen bonds : angle 5.87452 / 4.07 ( 2172) link_BETA1-4 : bond 0.00789 / 0.42 ( 12) link_BETA1-4 : angle 2.47008 / 1.58 ( 36) link_NAG-ASN : bond 0.00614 / 0.43 ( 47) link_NAG-ASN : angle 3.21302 / 2.17 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7472 (tp-100) REVERT: B 153 MET cc_start: 0.5390 (tmm) cc_final: 0.4669 (tpt) REVERT: B 726 ILE cc_start: 0.9442 (mp) cc_final: 0.9062 (mt) REVERT: B 900 MET cc_start: 0.8892 (mmm) cc_final: 0.8655 (mmm) REVERT: B 1029 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8377 (ttm) REVERT: A 41 LYS cc_start: 0.6213 (tmtt) cc_final: 0.5743 (mmmm) REVERT: A 118 LEU cc_start: 0.8645 (tp) cc_final: 0.8155 (mt) REVERT: A 133 PHE cc_start: 0.7410 (m-80) cc_final: 0.7044 (m-80) REVERT: A 177 MET cc_start: -0.0859 (tpt) cc_final: -0.1170 (tpt) REVERT: A 327 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 726 ILE cc_start: 0.9550 (mp) cc_final: 0.9325 (mt) REVERT: A 900 MET cc_start: 0.8909 (mmm) cc_final: 0.8654 (mmm) REVERT: A 1050 MET cc_start: 0.8347 (ptm) cc_final: 0.8052 (ptp) REVERT: C 134 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7872 (tp-100) REVERT: C 360 ASN cc_start: 0.8596 (m-40) cc_final: 0.8351 (m-40) REVERT: C 726 ILE cc_start: 0.9547 (mp) cc_final: 0.9220 (mt) outliers start: 48 outliers final: 19 residues processed: 169 average time/residue: 0.1432 time to fit residues: 41.2896 Evaluate side-chains 138 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 655 HIS A 784 GLN C 658 ASN ** C1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.113141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082929 restraints weight = 66510.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081371 restraints weight = 46485.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082066 restraints weight = 48280.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082699 restraints weight = 36885.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082801 restraints weight = 33069.659| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26466 Z= 0.127 Angle : 0.670 12.421 36116 Z= 0.321 Chirality : 0.050 1.207 4228 Planarity : 0.004 0.044 4565 Dihedral : 4.987 33.157 3415 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.76 % Allowed : 12.63 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.14), residues: 3150 helix: 0.30 (0.21), residues: 672 sheet: -0.97 (0.20), residues: 630 loop : -2.06 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.014 0.001 TYR A1067 PHE 0.023 0.001 PHE B 135 TRP 0.011 0.001 TRP C 104 HIS 0.004 0.001 HIS B1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (26365) covalent geometry : angle 0.63266 / 0.31 (35855) SS BOND : bond 0.00231 / 0.14 ( 42) SS BOND : angle 1.83363 / 1.30 ( 84) hydrogen bonds : bond 0.04087 / 2.72 ( 803) hydrogen bonds : angle 5.52596 / 3.82 ( 2172) link_BETA1-4 : bond 0.00880 / 0.53 ( 12) link_BETA1-4 : angle 2.36660 / 1.52 ( 36) link_NAG-ASN : bond 0.00520 / 0.36 ( 47) link_NAG-ASN : angle 3.10501 / 1.97 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5379 (tmm) cc_final: 0.4658 (tpt) REVERT: B 516 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: B 1029 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8220 (ttm) REVERT: A 41 LYS cc_start: 0.6222 (tmtt) cc_final: 0.5735 (mmmt) REVERT: A 327 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 462 LYS cc_start: 0.8139 (mptt) cc_final: 0.7565 (pttt) REVERT: A 516 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6469 (tt0) REVERT: A 726 ILE cc_start: 0.9495 (mp) cc_final: 0.9175 (mt) REVERT: A 1050 MET cc_start: 0.8355 (ptm) cc_final: 0.7871 (ptp) REVERT: C 360 ASN cc_start: 0.8638 (m-40) cc_final: 0.8397 (m-40) REVERT: C 462 LYS cc_start: 0.8042 (mptt) cc_final: 0.7340 (pttt) REVERT: C 516 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: C 726 ILE cc_start: 0.9512 (mp) cc_final: 0.9184 (mt) outliers start: 49 outliers final: 30 residues processed: 169 average time/residue: 0.1385 time to fit residues: 40.3472 Evaluate side-chains 154 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 262 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 210 optimal weight: 0.0270 chunk 119 optimal weight: 0.8980 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 564 GLN A 134 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.111519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081981 restraints weight = 66503.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080533 restraints weight = 47180.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081498 restraints weight = 52089.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081615 restraints weight = 37724.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082130 restraints weight = 33293.481| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26466 Z= 0.171 Angle : 0.669 11.576 36116 Z= 0.324 Chirality : 0.047 0.528 4228 Planarity : 0.004 0.044 4565 Dihedral : 4.944 28.277 3415 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.08 % Allowed : 14.14 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.14), residues: 3150 helix: 0.25 (0.20), residues: 672 sheet: -0.75 (0.20), residues: 624 loop : -2.05 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.017 0.001 TYR A1067 PHE 0.027 0.002 PHE A 133 TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS B1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (26365) covalent geometry : angle 0.63890 / 0.32 (35855) SS BOND : bond 0.00216 / 0.13 ( 42) SS BOND : angle 1.73033 / 1.22 ( 84) hydrogen bonds : bond 0.04403 / 2.92 ( 803) hydrogen bonds : angle 5.42305 / 3.76 ( 2172) link_BETA1-4 : bond 0.00699 / 0.40 ( 12) link_BETA1-4 : angle 2.30585 / 1.47 ( 36) link_NAG-ASN : bond 0.00521 / 0.36 ( 47) link_NAG-ASN : angle 2.78874 / 1.85 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4889 (tmm) cc_final: 0.4139 (tpt) REVERT: B 516 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: B 697 MET cc_start: 0.7900 (mtp) cc_final: 0.7637 (mtp) REVERT: B 1029 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8625 (ttm) REVERT: A 462 LYS cc_start: 0.8185 (mptt) cc_final: 0.7633 (pttt) REVERT: A 957 GLN cc_start: 0.8505 (tp40) cc_final: 0.8126 (tm-30) REVERT: C 360 ASN cc_start: 0.8553 (m-40) cc_final: 0.8227 (m-40) REVERT: C 462 LYS cc_start: 0.8064 (mptt) cc_final: 0.7369 (pttt) outliers start: 58 outliers final: 35 residues processed: 178 average time/residue: 0.1344 time to fit residues: 41.3730 Evaluate side-chains 155 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 222 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 123 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 302 optimal weight: 0.6980 chunk 183 optimal weight: 0.0570 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 259 optimal weight: 0.0970 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 709 ASN B 787 GLN B 935 GLN A 134 GLN A 787 GLN A 935 GLN C 787 GLN C 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.114376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084165 restraints weight = 66138.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082959 restraints weight = 42225.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083835 restraints weight = 43654.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084018 restraints weight = 33790.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084364 restraints weight = 29825.233| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26466 Z= 0.103 Angle : 0.614 14.078 36116 Z= 0.296 Chirality : 0.045 0.318 4228 Planarity : 0.003 0.044 4565 Dihedral : 4.629 27.294 3415 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.83 % Allowed : 15.07 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3150 helix: 0.83 (0.22), residues: 657 sheet: -0.41 (0.21), residues: 579 loop : -1.91 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1091 TYR 0.011 0.001 TYR B1067 PHE 0.024 0.001 PHE A 133 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (26365) covalent geometry : angle 0.58707 / 0.29 (35855) SS BOND : bond 0.00177 / 0.12 ( 42) SS BOND : angle 1.41161 / 0.94 ( 84) hydrogen bonds : bond 0.03278 / 2.20 ( 803) hydrogen bonds : angle 5.08165 / 3.53 ( 2172) link_BETA1-4 : bond 0.00891 / 0.52 ( 12) link_BETA1-4 : angle 2.27321 / 1.45 ( 36) link_NAG-ASN : bond 0.00519 / 0.37 ( 47) link_NAG-ASN : angle 2.51457 / 1.67 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4814 (tmm) cc_final: 0.4502 (tmm) REVERT: B 516 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: B 697 MET cc_start: 0.7826 (mtp) cc_final: 0.7567 (mtp) REVERT: B 916 LEU cc_start: 0.8471 (tp) cc_final: 0.8157 (tp) REVERT: A 462 LYS cc_start: 0.8186 (mptt) cc_final: 0.7278 (pttt) REVERT: A 465 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: C 177 MET cc_start: -0.0973 (tpt) cc_final: -0.1192 (tpt) REVERT: C 360 ASN cc_start: 0.8585 (m-40) cc_final: 0.8379 (m-40) REVERT: C 462 LYS cc_start: 0.8068 (mptt) cc_final: 0.7223 (pttt) REVERT: C 465 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6511 (mp0) outliers start: 51 outliers final: 23 residues processed: 184 average time/residue: 0.1494 time to fit residues: 46.3558 Evaluate side-chains 150 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 33 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 310 optimal weight: 0.0770 chunk 24 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN B 784 GLN A 134 GLN A 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.111995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082598 restraints weight = 66751.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.080490 restraints weight = 48305.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081303 restraints weight = 52619.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081797 restraints weight = 37194.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082125 restraints weight = 33439.583| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26466 Z= 0.169 Angle : 0.645 11.897 36116 Z= 0.314 Chirality : 0.046 0.313 4228 Planarity : 0.004 0.043 4565 Dihedral : 4.719 27.652 3415 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.61 % Allowed : 15.82 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3150 helix: 0.68 (0.21), residues: 657 sheet: -0.47 (0.20), residues: 627 loop : -1.92 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 355 TYR 0.015 0.001 TYR A1067 PHE 0.022 0.001 PHE B 429 TRP 0.006 0.001 TRP C1102 HIS 0.002 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (26365) covalent geometry : angle 0.61691 / 0.31 (35855) SS BOND : bond 0.00227 / 0.13 ( 42) SS BOND : angle 1.63638 / 1.08 ( 84) hydrogen bonds : bond 0.04027 / 2.68 ( 803) hydrogen bonds : angle 5.16959 / 3.59 ( 2172) link_BETA1-4 : bond 0.00682 / 0.38 ( 12) link_BETA1-4 : angle 2.27391 / 1.44 ( 36) link_NAG-ASN : bond 0.00491 / 0.35 ( 47) link_NAG-ASN : angle 2.59934 / 1.74 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4695 (tmm) cc_final: 0.4341 (tmm) REVERT: B 516 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: B 697 MET cc_start: 0.7911 (mtp) cc_final: 0.7650 (mtp) REVERT: A 462 LYS cc_start: 0.8161 (mptt) cc_final: 0.7232 (pttt) REVERT: A 465 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: C 360 ASN cc_start: 0.8528 (m-40) cc_final: 0.8215 (m-40) REVERT: C 462 LYS cc_start: 0.8066 (mptt) cc_final: 0.7219 (pttt) REVERT: C 465 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6368 (mp0) outliers start: 45 outliers final: 28 residues processed: 167 average time/residue: 0.1458 time to fit residues: 42.2306 Evaluate side-chains 152 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 138 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 240 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.113085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083301 restraints weight = 66550.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081610 restraints weight = 45560.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082493 restraints weight = 45972.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082771 restraints weight = 34797.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083007 restraints weight = 31997.935| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26466 Z= 0.114 Angle : 0.610 12.388 36116 Z= 0.295 Chirality : 0.045 0.303 4228 Planarity : 0.003 0.043 4565 Dihedral : 4.596 28.633 3415 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.47 % Allowed : 16.22 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3150 helix: 0.81 (0.21), residues: 657 sheet: -0.43 (0.20), residues: 615 loop : -1.86 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 905 TYR 0.013 0.001 TYR A1067 PHE 0.020 0.001 PHE A 133 TRP 0.009 0.001 TRP A 104 HIS 0.004 0.000 HIS A1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (26365) covalent geometry : angle 0.58170 / 0.29 (35855) SS BOND : bond 0.00177 / 0.12 ( 42) SS BOND : angle 1.38230 / 0.91 ( 84) hydrogen bonds : bond 0.03572 / 2.39 ( 803) hydrogen bonds : angle 5.03654 / 3.50 ( 2172) link_BETA1-4 : bond 0.00799 / 0.45 ( 12) link_BETA1-4 : angle 2.26487 / 1.43 ( 36) link_NAG-ASN : bond 0.00491 / 0.35 ( 47) link_NAG-ASN : angle 2.63119 / 1.76 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4741 (tmm) cc_final: 0.4314 (tmm) REVERT: B 516 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: B 697 MET cc_start: 0.7896 (mtp) cc_final: 0.7651 (mtp) REVERT: B 916 LEU cc_start: 0.8472 (tp) cc_final: 0.8157 (tp) REVERT: A 462 LYS cc_start: 0.8178 (mptt) cc_final: 0.7267 (pttt) REVERT: A 465 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: C 462 LYS cc_start: 0.8079 (mptt) cc_final: 0.7333 (mttt) REVERT: C 465 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6621 (mp0) outliers start: 41 outliers final: 29 residues processed: 165 average time/residue: 0.1416 time to fit residues: 40.3320 Evaluate side-chains 154 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 292 optimal weight: 5.9990 chunk 160 optimal weight: 0.0980 chunk 145 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 155 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 274 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 709 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.112823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083802 restraints weight = 67178.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081546 restraints weight = 50224.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082391 restraints weight = 53755.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083037 restraints weight = 37668.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083218 restraints weight = 33864.605| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26466 Z= 0.128 Angle : 0.623 12.400 36116 Z= 0.300 Chirality : 0.045 0.301 4228 Planarity : 0.004 0.043 4565 Dihedral : 4.575 25.760 3415 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.44 % Allowed : 16.58 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3150 helix: 0.83 (0.21), residues: 657 sheet: -0.46 (0.20), residues: 627 loop : -1.84 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 905 TYR 0.014 0.001 TYR A1067 PHE 0.024 0.001 PHE B 429 TRP 0.007 0.001 TRP A 104 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26365) covalent geometry : angle 0.59159 / 0.29 (35855) SS BOND : bond 0.00223 / 0.14 ( 42) SS BOND : angle 1.36836 / 0.92 ( 84) hydrogen bonds : bond 0.03683 / 2.46 ( 803) hydrogen bonds : angle 5.00079 / 3.47 ( 2172) link_BETA1-4 : bond 0.00767 / 0.43 ( 12) link_BETA1-4 : angle 2.26140 / 1.43 ( 36) link_NAG-ASN : bond 0.00470 / 0.33 ( 47) link_NAG-ASN : angle 2.80716 / 1.97 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4725 (tmm) cc_final: 0.4306 (tmm) REVERT: B 516 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7188 (tm-30) REVERT: B 697 MET cc_start: 0.7900 (mtp) cc_final: 0.7653 (mtp) REVERT: B 904 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: B 916 LEU cc_start: 0.8466 (tp) cc_final: 0.8178 (tp) REVERT: B 1029 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8470 (ttm) REVERT: A 462 LYS cc_start: 0.8206 (mptt) cc_final: 0.7276 (pttt) REVERT: A 465 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: C 462 LYS cc_start: 0.8027 (mptt) cc_final: 0.7312 (mttt) REVERT: C 465 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6567 (mp0) outliers start: 40 outliers final: 34 residues processed: 166 average time/residue: 0.1402 time to fit residues: 39.5910 Evaluate side-chains 162 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 82 optimal weight: 2.9990 chunk 211 optimal weight: 0.0270 chunk 122 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 264 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 171 optimal weight: 0.0030 chunk 18 optimal weight: 4.9990 overall best weight: 1.8054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 709 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.111645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082612 restraints weight = 67169.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080284 restraints weight = 51708.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081268 restraints weight = 54169.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081824 restraints weight = 38333.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082021 restraints weight = 34715.363| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26466 Z= 0.166 Angle : 0.648 12.731 36116 Z= 0.314 Chirality : 0.046 0.321 4228 Planarity : 0.004 0.043 4565 Dihedral : 4.699 28.273 3415 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.36 % Allowed : 16.97 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3150 helix: 0.68 (0.21), residues: 675 sheet: -0.45 (0.20), residues: 636 loop : -1.90 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.015 0.001 TYR A1067 PHE 0.023 0.001 PHE B 429 TRP 0.006 0.001 TRP C1102 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (26365) covalent geometry : angle 0.62145 / 0.31 (35855) SS BOND : bond 0.00250 / 0.15 ( 42) SS BOND : angle 1.43164 / 0.95 ( 84) hydrogen bonds : bond 0.04067 / 2.71 ( 803) hydrogen bonds : angle 5.10363 / 3.54 ( 2172) link_BETA1-4 : bond 0.00733 / 0.40 ( 12) link_BETA1-4 : angle 2.29035 / 1.44 ( 36) link_NAG-ASN : bond 0.00459 / 0.32 ( 47) link_NAG-ASN : angle 2.59113 / 1.75 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4596 (tmm) cc_final: 0.4161 (tmm) REVERT: B 516 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: B 697 MET cc_start: 0.7925 (mtp) cc_final: 0.7676 (mtp) REVERT: B 904 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: A 462 LYS cc_start: 0.8194 (mptt) cc_final: 0.7305 (mttt) REVERT: A 465 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: C 462 LYS cc_start: 0.8035 (mptt) cc_final: 0.7327 (mttt) REVERT: C 465 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6507 (mp0) outliers start: 38 outliers final: 32 residues processed: 158 average time/residue: 0.1250 time to fit residues: 34.0914 Evaluate side-chains 158 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 273 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 0.0040 chunk 186 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 297 optimal weight: 0.1980 chunk 222 optimal weight: 9.9990 chunk 251 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 overall best weight: 1.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.111435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082422 restraints weight = 66800.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080211 restraints weight = 51132.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081145 restraints weight = 53498.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081522 restraints weight = 38581.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081823 restraints weight = 35449.002| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26466 Z= 0.167 Angle : 0.640 12.150 36116 Z= 0.311 Chirality : 0.046 0.320 4228 Planarity : 0.004 0.043 4565 Dihedral : 4.719 32.337 3414 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.58 % Allowed : 16.86 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3150 helix: 0.64 (0.21), residues: 675 sheet: -0.50 (0.20), residues: 636 loop : -1.90 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.016 0.001 TYR A1067 PHE 0.024 0.001 PHE B 429 TRP 0.007 0.001 TRP C1102 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (26365) covalent geometry : angle 0.61411 / 0.31 (35855) SS BOND : bond 0.00252 / 0.15 ( 42) SS BOND : angle 1.42587 / 0.95 ( 84) hydrogen bonds : bond 0.04022 / 2.68 ( 803) hydrogen bonds : angle 5.09328 / 3.53 ( 2172) link_BETA1-4 : bond 0.00766 / 0.44 ( 12) link_BETA1-4 : angle 2.30699 / 1.45 ( 36) link_NAG-ASN : bond 0.00489 / 0.35 ( 47) link_NAG-ASN : angle 2.52178 / 1.68 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.20 seconds wall clock time: 57 minutes 39.61 seconds (3459.61 seconds total)