Starting phenix.real_space_refine on Thu Mar 5 23:03:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhh_31994/03_2026/7vhh_31994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhh_31994/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vhh_31994/03_2026/7vhh_31994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhh_31994/03_2026/7vhh_31994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vhh_31994/03_2026/7vhh_31994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhh_31994/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 33 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 dihedrals: 36 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.09, per 1000 atoms: 0.24 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 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: 1.17 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: 5.56 Time building geometry restraints manager: 2.87 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 - 22.31: 15422 22.31 - 44.63: 887 44.63 - 66.94: 107 66.94 - 89.25: 28 89.25 - 111.57: 32 Dihedral angle restraints: 16476 sinusoidal: 7191 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 16473 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.620 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 14.511 111.567 10374 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 covalent geometry : bond 0.00586 (26365) covalent geometry : angle 0.83296 (35855) SS BOND : bond 0.00604 ( 42) SS BOND : angle 1.28052 ( 84) hydrogen bonds : bond 0.27047 ( 803) hydrogen bonds : angle 9.68601 ( 2172) link_BETA1-4 : bond 0.01283 ( 12) link_BETA1-4 : angle 4.10726 ( 36) link_NAG-ASN : bond 0.01543 ( 47) link_NAG-ASN : angle 4.42753 ( 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 : 0.873 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: 0.1886 time to fit residues: 70.2154 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 : 0.959 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 709 ASN B 784 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083211 restraints weight = 67221.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080865 restraints weight = 54031.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081683 restraints weight = 59480.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082160 restraints weight = 41870.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082303 restraints weight = 38401.121| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26466 Z= 0.187 Angle : 0.823 16.324 36116 Z= 0.388 Chirality : 0.053 0.989 4228 Planarity : 0.005 0.047 4565 Dihedral : 10.180 95.361 4664 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.93 % Allowed : 8.04 % Favored : 91.03 % 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: -0.36 (0.20), residues: 672 sheet: -0.69 (0.21), residues: 624 loop : -2.34 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.016 0.001 TYR A 904 PHE 0.035 0.002 PHE B 133 TRP 0.017 0.001 TRP B 104 HIS 0.006 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00428 (26365) covalent geometry : angle 0.77280 (35855) SS BOND : bond 0.00232 ( 42) SS BOND : angle 1.98956 ( 84) hydrogen bonds : bond 0.05863 ( 803) hydrogen bonds : angle 6.44030 ( 2172) link_BETA1-4 : bond 0.00933 ( 12) link_BETA1-4 : angle 3.72383 ( 36) link_NAG-ASN : bond 0.00695 ( 47) link_NAG-ASN : angle 3.96096 ( 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 174 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5541 (tmm) cc_final: 0.4944 (tpt) REVERT: B 177 MET cc_start: -0.0918 (tpt) cc_final: -0.1344 (tpt) REVERT: B 565 PHE cc_start: 0.7969 (m-80) cc_final: 0.7660 (m-10) REVERT: B 592 PHE cc_start: 0.6790 (t80) cc_final: 0.6480 (t80) REVERT: B 726 ILE cc_start: 0.9476 (mp) cc_final: 0.9080 (mt) REVERT: A 41 LYS cc_start: 0.6233 (tmtt) cc_final: 0.5837 (mmmm) REVERT: A 118 LEU cc_start: 0.8571 (tp) cc_final: 0.8198 (mt) REVERT: A 133 PHE cc_start: 0.7547 (m-80) cc_final: 0.7119 (m-80) REVERT: A 177 MET cc_start: -0.1172 (tpt) cc_final: -0.1522 (tpt) REVERT: A 726 ILE cc_start: 0.9564 (mp) cc_final: 0.9353 (mt) REVERT: A 1050 MET cc_start: 0.8538 (ptm) cc_final: 0.8247 (ptp) REVERT: C 360 ASN cc_start: 0.8583 (m-40) cc_final: 0.8346 (m-40) REVERT: C 726 ILE cc_start: 0.9549 (mp) cc_final: 0.9218 (mt) outliers start: 26 outliers final: 14 residues processed: 166 average time/residue: 0.1588 time to fit residues: 43.7207 Evaluate side-chains 129 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 73 optimal weight: 0.0670 chunk 263 optimal weight: 5.9990 chunk 288 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 655 HIS A 134 GLN A 895 GLN C 134 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.110100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081384 restraints weight = 67445.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.079357 restraints weight = 57715.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080180 restraints weight = 63169.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080963 restraints weight = 42268.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081356 restraints weight = 37146.321| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 26466 Z= 0.261 Angle : 0.797 15.054 36116 Z= 0.383 Chirality : 0.052 0.730 4228 Planarity : 0.005 0.047 4565 Dihedral : 8.941 97.659 4654 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.94 % Allowed : 11.84 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.37 (0.14), residues: 3150 helix: -0.22 (0.20), residues: 651 sheet: -1.21 (0.20), residues: 681 loop : -2.32 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 44 TYR 0.022 0.001 TYR A1067 PHE 0.030 0.002 PHE B 157 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00616 (26365) covalent geometry : angle 0.75373 (35855) SS BOND : bond 0.00516 ( 42) SS BOND : angle 2.14335 ( 84) hydrogen bonds : bond 0.05601 ( 803) hydrogen bonds : angle 6.12575 ( 2172) link_BETA1-4 : bond 0.00790 ( 12) link_BETA1-4 : angle 3.03007 ( 36) link_NAG-ASN : bond 0.00631 ( 47) link_NAG-ASN : angle 3.61179 ( 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 182 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7516 (tp-100) REVERT: B 153 MET cc_start: 0.5341 (tmm) cc_final: 0.4592 (tpt) REVERT: B 177 MET cc_start: -0.0699 (tpt) cc_final: -0.0965 (tpt) REVERT: B 565 PHE cc_start: 0.7953 (m-10) cc_final: 0.7746 (m-10) REVERT: B 726 ILE cc_start: 0.9460 (mp) cc_final: 0.9100 (mt) REVERT: B 1029 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8351 (ttm) REVERT: A 41 LYS cc_start: 0.6159 (tmtt) cc_final: 0.5634 (mmmm) REVERT: A 153 MET cc_start: 0.5048 (tmm) cc_final: 0.4701 (tpt) REVERT: A 177 MET cc_start: -0.1139 (tpt) cc_final: -0.1413 (tpt) REVERT: A 726 ILE cc_start: 0.9552 (mp) cc_final: 0.9342 (mt) REVERT: A 1050 MET cc_start: 0.8514 (ptm) cc_final: 0.8191 (ptp) REVERT: C 360 ASN cc_start: 0.8569 (m-40) cc_final: 0.8336 (m-40) REVERT: C 726 ILE cc_start: 0.9540 (mp) cc_final: 0.9223 (mt) outliers start: 54 outliers final: 28 residues processed: 172 average time/residue: 0.1342 time to fit residues: 39.6580 Evaluate side-chains 141 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL 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 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 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 642 VAL 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 312 ILE 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 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 293 optimal weight: 0.0070 chunk 307 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 709 ASN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.113066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083166 restraints weight = 66156.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081269 restraints weight = 45916.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082350 restraints weight = 51050.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082415 restraints weight = 37943.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082876 restraints weight = 33214.391| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26466 Z= 0.114 Angle : 0.662 12.802 36116 Z= 0.320 Chirality : 0.047 0.451 4228 Planarity : 0.004 0.046 4565 Dihedral : 7.980 90.873 4654 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.54 % Allowed : 13.63 % Favored : 84.82 % 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: -1.96 (0.14), residues: 3150 helix: 0.20 (0.21), residues: 672 sheet: -0.86 (0.20), residues: 633 loop : -2.14 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.012 0.001 TYR A1067 PHE 0.028 0.001 PHE A 133 TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00253 (26365) covalent geometry : angle 0.62333 (35855) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.62626 ( 84) hydrogen bonds : bond 0.04032 ( 803) hydrogen bonds : angle 5.53686 ( 2172) link_BETA1-4 : bond 0.00859 ( 12) link_BETA1-4 : angle 2.95178 ( 36) link_NAG-ASN : bond 0.00623 ( 47) link_NAG-ASN : angle 3.08545 ( 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 173 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5247 (tmm) cc_final: 0.4501 (tpt) REVERT: B 516 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: B 726 ILE cc_start: 0.9420 (mp) cc_final: 0.9055 (mt) REVERT: B 902 MET cc_start: 0.9387 (mmt) cc_final: 0.9169 (mmt) REVERT: B 1029 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8270 (ttm) REVERT: A 41 LYS cc_start: 0.6248 (tmtt) cc_final: 0.5823 (mmmm) REVERT: A 134 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7654 (tp-100) REVERT: A 153 MET cc_start: 0.4895 (tmm) cc_final: 0.4535 (tpt) REVERT: A 462 LYS cc_start: 0.8138 (mptt) cc_final: 0.7566 (pttt) REVERT: A 516 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: A 726 ILE cc_start: 0.9506 (mp) cc_final: 0.9192 (mt) REVERT: A 1050 MET cc_start: 0.8349 (ptm) cc_final: 0.7895 (ptp) REVERT: C 134 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7898 (tp-100) REVERT: C 360 ASN cc_start: 0.8663 (m-40) cc_final: 0.8408 (m-40) REVERT: C 462 LYS cc_start: 0.8040 (mptt) cc_final: 0.7339 (pttt) REVERT: C 516 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6320 (tt0) REVERT: C 726 ILE cc_start: 0.9516 (mp) cc_final: 0.9189 (mt) REVERT: C 904 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6588 (m-80) outliers start: 43 outliers final: 21 residues processed: 161 average time/residue: 0.1394 time to fit residues: 38.3141 Evaluate side-chains 149 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 200 TYR 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 710 ASN Chi-restraints excluded: chain B residue 906 PHE 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 382 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain C residue 127 VAL 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 436 TRP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 904 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 262 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 260 optimal weight: 0.7980 chunk 317 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN A 784 GLN A 895 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 = 0.3765 r_free = 0.3765 target = 0.110980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081559 restraints weight = 66904.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079213 restraints weight = 49417.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079919 restraints weight = 56512.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080590 restraints weight = 39898.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080722 restraints weight = 35973.973| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26466 Z= 0.197 Angle : 0.705 13.671 36116 Z= 0.338 Chirality : 0.050 1.068 4228 Planarity : 0.004 0.044 4565 Dihedral : 8.053 94.105 4654 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.33 % Allowed : 14.57 % 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: -1.98 (0.14), residues: 3150 helix: 0.11 (0.20), residues: 672 sheet: -0.79 (0.20), residues: 606 loop : -2.14 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.018 0.001 TYR A1067 PHE 0.021 0.002 PHE A 133 TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00469 (26365) covalent geometry : angle 0.66513 (35855) SS BOND : bond 0.00220 ( 42) SS BOND : angle 1.85258 ( 84) hydrogen bonds : bond 0.04605 ( 803) hydrogen bonds : angle 5.53211 ( 2172) link_BETA1-4 : bond 0.00760 ( 12) link_BETA1-4 : angle 2.83695 ( 36) link_NAG-ASN : bond 0.00565 ( 47) link_NAG-ASN : angle 3.24644 ( 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: 65 poor density : 124 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5150 (tmm) cc_final: 0.4389 (tpt) REVERT: B 516 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: B 959 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.8844 (tt) REVERT: B 1029 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8199 (ttm) REVERT: A 153 MET cc_start: 0.4959 (tmm) cc_final: 0.4592 (tpt) REVERT: A 462 LYS cc_start: 0.8136 (mptt) cc_final: 0.7198 (pttt) REVERT: A 465 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: A 516 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: A 900 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8030 (mmm) REVERT: C 360 ASN cc_start: 0.8615 (m-40) cc_final: 0.8407 (m-40) REVERT: C 462 LYS cc_start: 0.8094 (mptt) cc_final: 0.7378 (pttt) outliers start: 65 outliers final: 38 residues processed: 174 average time/residue: 0.1431 time to fit residues: 43.2620 Evaluate side-chains 159 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 959 LEU 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 171 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 436 TRP 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 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 900 MET 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 208 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 222 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 302 optimal weight: 0.6980 chunk 183 optimal weight: 0.0040 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.111695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081935 restraints weight = 66430.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.079876 restraints weight = 45888.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080688 restraints weight = 49086.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081368 restraints weight = 35565.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081521 restraints weight = 31611.882| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26466 Z= 0.151 Angle : 0.649 13.295 36116 Z= 0.313 Chirality : 0.046 0.710 4228 Planarity : 0.004 0.045 4565 Dihedral : 7.652 90.933 4654 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.33 % Allowed : 15.50 % Favored : 82.17 % 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: -1.83 (0.14), residues: 3150 helix: 0.28 (0.21), residues: 672 sheet: -0.69 (0.21), residues: 603 loop : -2.06 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1107 TYR 0.015 0.001 TYR A1067 PHE 0.019 0.001 PHE A 133 TRP 0.010 0.001 TRP B 104 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00353 (26365) covalent geometry : angle 0.61349 (35855) SS BOND : bond 0.00222 ( 42) SS BOND : angle 1.53445 ( 84) hydrogen bonds : bond 0.04093 ( 803) hydrogen bonds : angle 5.34843 ( 2172) link_BETA1-4 : bond 0.00804 ( 12) link_BETA1-4 : angle 2.78192 ( 36) link_NAG-ASN : bond 0.00516 ( 47) link_NAG-ASN : angle 2.96494 ( 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 187 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 122 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5057 (tmm) cc_final: 0.4298 (tpt) REVERT: B 516 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: B 959 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.8762 (tt) REVERT: B 1029 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8295 (ttm) REVERT: A 153 MET cc_start: 0.4851 (tmm) cc_final: 0.4485 (tpt) REVERT: A 177 MET cc_start: -0.1475 (tpt) cc_final: -0.1785 (tpt) REVERT: A 462 LYS cc_start: 0.8140 (mptt) cc_final: 0.7579 (pttt) REVERT: A 516 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: A 957 GLN cc_start: 0.8448 (tp40) cc_final: 0.8130 (tm-30) REVERT: C 360 ASN cc_start: 0.8608 (m-40) cc_final: 0.8405 (m-40) REVERT: C 462 LYS cc_start: 0.8046 (mptt) cc_final: 0.7155 (pttt) REVERT: C 465 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6393 (mp0) outliers start: 65 outliers final: 39 residues processed: 176 average time/residue: 0.1519 time to fit residues: 46.7454 Evaluate side-chains 162 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR 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 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU 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 382 VAL Chi-restraints excluded: chain A residue 436 TRP 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 738 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 436 TRP 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 Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 33 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 73 optimal weight: 0.0020 chunk 216 optimal weight: 0.5980 chunk 310 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 289 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083960 restraints weight = 66103.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082420 restraints weight = 54345.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083225 restraints weight = 47332.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.083456 restraints weight = 38029.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.083593 restraints weight = 35405.556| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26466 Z= 0.103 Angle : 0.604 14.473 36116 Z= 0.292 Chirality : 0.045 0.420 4228 Planarity : 0.003 0.044 4565 Dihedral : 7.103 85.897 4654 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.19 % Allowed : 15.97 % Favored : 81.84 % 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: -1.50 (0.14), residues: 3150 helix: 0.78 (0.21), residues: 657 sheet: -0.54 (0.20), residues: 639 loop : -1.92 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.011 0.001 TYR A1067 PHE 0.021 0.001 PHE B 429 TRP 0.011 0.001 TRP B 104 HIS 0.003 0.000 HIS B1118 Details of bonding type rmsd covalent geometry : bond 0.00228 (26365) covalent geometry : angle 0.57143 (35855) SS BOND : bond 0.00283 ( 42) SS BOND : angle 1.20260 ( 84) hydrogen bonds : bond 0.03330 ( 803) hydrogen bonds : angle 5.02201 ( 2172) link_BETA1-4 : bond 0.00846 ( 12) link_BETA1-4 : angle 2.73211 ( 36) link_NAG-ASN : bond 0.00568 ( 47) link_NAG-ASN : angle 2.77483 ( 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 204 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4802 (tmm) cc_final: 0.4460 (tmm) REVERT: B 516 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: B 697 MET cc_start: 0.7864 (mtp) cc_final: 0.7576 (mtp) REVERT: B 916 LEU cc_start: 0.8524 (tp) cc_final: 0.8272 (tt) REVERT: A 153 MET cc_start: 0.4603 (tmm) cc_final: 0.4177 (tpt) REVERT: A 462 LYS cc_start: 0.8190 (mptt) cc_final: 0.7272 (pttt) REVERT: A 465 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: A 900 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7898 (mmm) REVERT: C 462 LYS cc_start: 0.8086 (mptt) cc_final: 0.7253 (pttt) REVERT: C 465 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6513 (mp0) outliers start: 61 outliers final: 32 residues processed: 193 average time/residue: 0.1477 time to fit residues: 49.3886 Evaluate side-chains 164 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR 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 642 VAL Chi-restraints excluded: chain B residue 754 LEU 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 465 GLU Chi-restraints excluded: chain A residue 515 PHE 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 738 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 120 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 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 906 PHE 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: 6.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.111484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082001 restraints weight = 66836.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079733 restraints weight = 48223.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.080615 restraints weight = 51311.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081096 restraints weight = 37082.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081347 restraints weight = 33817.250| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26466 Z= 0.178 Angle : 0.658 14.710 36116 Z= 0.319 Chirality : 0.045 0.425 4228 Planarity : 0.004 0.043 4565 Dihedral : 7.244 87.937 4654 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.72 % Allowed : 16.90 % Favored : 81.38 % 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: -1.56 (0.14), residues: 3150 helix: 0.66 (0.21), residues: 657 sheet: -0.55 (0.20), residues: 645 loop : -1.95 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.016 0.001 TYR A1067 PHE 0.017 0.001 PHE B 135 TRP 0.010 0.001 TRP A 258 HIS 0.003 0.001 HIS A1118 Details of bonding type rmsd covalent geometry : bond 0.00421 (26365) covalent geometry : angle 0.62247 (35855) SS BOND : bond 0.00256 ( 42) SS BOND : angle 1.64960 ( 84) hydrogen bonds : bond 0.04133 ( 803) hydrogen bonds : angle 5.17880 ( 2172) link_BETA1-4 : bond 0.00697 ( 12) link_BETA1-4 : angle 2.73306 ( 36) link_NAG-ASN : bond 0.00492 ( 47) link_NAG-ASN : angle 2.98149 ( 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 173 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4840 (tmm) cc_final: 0.4427 (tmm) REVERT: B 516 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: B 697 MET cc_start: 0.7931 (mtp) cc_final: 0.7655 (mtp) REVERT: A 153 MET cc_start: 0.4610 (tmm) cc_final: 0.4188 (tpt) REVERT: A 462 LYS cc_start: 0.8148 (mptt) cc_final: 0.7204 (pttt) REVERT: A 465 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: A 900 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.7976 (mmm) REVERT: C 462 LYS cc_start: 0.8068 (mptt) cc_final: 0.7225 (pttt) REVERT: C 465 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: C 754 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8918 (tp) outliers start: 48 outliers final: 38 residues processed: 166 average time/residue: 0.1448 time to fit residues: 41.5673 Evaluate side-chains 163 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL 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 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 754 LEU 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 465 GLU 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 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 120 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 410 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 754 LEU Chi-restraints excluded: chain C residue 906 PHE 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: 3.9990 chunk 160 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 73 optimal weight: 0.0060 chunk 274 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.112659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083079 restraints weight = 66998.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081305 restraints weight = 47104.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082532 restraints weight = 52770.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082397 restraints weight = 38259.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082631 restraints weight = 33922.808| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3114 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= 0.123 Angle : 0.624 15.305 36116 Z= 0.300 Chirality : 0.044 0.348 4228 Planarity : 0.003 0.044 4565 Dihedral : 7.025 84.334 4654 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.79 % Allowed : 17.12 % Favored : 81.09 % 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: -1.46 (0.14), residues: 3150 helix: 0.79 (0.21), residues: 657 sheet: -0.49 (0.20), residues: 630 loop : -1.89 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.014 0.001 TYR A1067 PHE 0.018 0.001 PHE B 135 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.000 HIS A1118 Details of bonding type rmsd covalent geometry : bond 0.00286 (26365) covalent geometry : angle 0.58652 (35855) SS BOND : bond 0.00170 ( 42) SS BOND : angle 1.41940 ( 84) hydrogen bonds : bond 0.03640 ( 803) hydrogen bonds : angle 5.03458 ( 2172) link_BETA1-4 : bond 0.00768 ( 12) link_BETA1-4 : angle 2.72328 ( 36) link_NAG-ASN : bond 0.00498 ( 47) link_NAG-ASN : angle 3.03764 ( 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 180 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4732 (tmm) cc_final: 0.4268 (tmm) REVERT: B 516 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: B 697 MET cc_start: 0.7914 (mtp) cc_final: 0.7630 (mtp) REVERT: B 916 LEU cc_start: 0.8418 (tp) cc_final: 0.8116 (tp) REVERT: A 153 MET cc_start: 0.4579 (tmm) cc_final: 0.4158 (tpt) REVERT: A 462 LYS cc_start: 0.8162 (mptt) cc_final: 0.7209 (pttt) REVERT: A 465 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: A 900 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: C 462 LYS cc_start: 0.8086 (mptt) cc_final: 0.7233 (pttt) REVERT: C 465 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6376 (mp0) REVERT: C 904 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.6655 (m-80) outliers start: 50 outliers final: 44 residues processed: 173 average time/residue: 0.1473 time to fit residues: 44.1233 Evaluate side-chains 174 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL 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 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE 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 302 THR 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 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 120 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 410 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 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 906 PHE 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: 4.9990 chunk 211 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 171 optimal weight: 0.0060 chunk 18 optimal weight: 6.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080235 restraints weight = 67387.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077530 restraints weight = 52790.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078304 restraints weight = 54356.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079364 restraints weight = 40212.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079396 restraints weight = 34754.000| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 26466 Z= 0.283 Angle : 0.763 16.598 36116 Z= 0.372 Chirality : 0.048 0.436 4228 Planarity : 0.005 0.043 4565 Dihedral : 7.775 87.582 4654 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.12 % Allowed : 17.08 % Favored : 80.80 % 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: 0.16 (0.20), residues: 690 sheet: -0.63 (0.20), residues: 600 loop : -2.06 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 905 TYR 0.021 0.002 TYR A1067 PHE 0.018 0.002 PHE B 135 TRP 0.009 0.001 TRP C1102 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00671 (26365) covalent geometry : angle 0.72578 (35855) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.77872 ( 84) hydrogen bonds : bond 0.05155 ( 803) hydrogen bonds : angle 5.47744 ( 2172) link_BETA1-4 : bond 0.00635 ( 12) link_BETA1-4 : angle 2.85837 ( 36) link_NAG-ASN : bond 0.00548 ( 47) link_NAG-ASN : angle 3.34636 ( 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 174 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 115 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4960 (tmm) cc_final: 0.4512 (tmm) REVERT: B 516 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: B 1029 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8639 (ttt) REVERT: A 153 MET cc_start: 0.4613 (tmm) cc_final: 0.4137 (tpt) REVERT: A 462 LYS cc_start: 0.8109 (mptt) cc_final: 0.7186 (pttt) REVERT: A 465 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: A 900 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7853 (mmm) REVERT: C 462 LYS cc_start: 0.8023 (mptt) cc_final: 0.7189 (pttt) REVERT: C 465 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6331 (mp0) outliers start: 59 outliers final: 47 residues processed: 168 average time/residue: 0.1510 time to fit residues: 43.9518 Evaluate side-chains 164 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL 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 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE 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 302 THR 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 572 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 A residue 853 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 120 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 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 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 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 906 PHE 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: 0.8980 chunk 43 optimal weight: 7.9990 chunk 73 optimal weight: 0.0070 chunk 186 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 297 optimal weight: 0.2980 chunk 222 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 302 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.111086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081742 restraints weight = 66756.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.079539 restraints weight = 49424.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080407 restraints weight = 52446.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081003 restraints weight = 37696.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081154 restraints weight = 34060.437| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26466 Z= 0.158 Angle : 0.682 18.956 36116 Z= 0.328 Chirality : 0.047 0.881 4228 Planarity : 0.004 0.044 4565 Dihedral : 7.563 82.881 4654 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.94 % Allowed : 17.37 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3150 helix: 0.35 (0.20), residues: 690 sheet: -0.60 (0.20), residues: 615 loop : -2.02 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 905 TYR 0.016 0.001 TYR A1067 PHE 0.023 0.001 PHE B 592 TRP 0.009 0.001 TRP B 104 HIS 0.003 0.000 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00372 (26365) covalent geometry : angle 0.63813 (35855) SS BOND : bond 0.00230 ( 42) SS BOND : angle 1.50601 ( 84) hydrogen bonds : bond 0.04153 ( 803) hydrogen bonds : angle 5.20654 ( 2172) link_BETA1-4 : bond 0.00726 ( 12) link_BETA1-4 : angle 2.81195 ( 36) link_NAG-ASN : bond 0.00600 ( 47) link_NAG-ASN : angle 3.49202 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.88 seconds wall clock time: 60 minutes 10.94 seconds (3610.94 seconds total)