Starting phenix.real_space_refine on Tue Oct 27 13:16:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cab_30325/10_2026/7cab_30325.map" } resolution = 3.52 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 111 5.16 5 C 15894 2.51 5 N 4080 2.21 5 O 4893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24978 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8046 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8046 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8046 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.12, per 1000 atoms: 0.25 Number of scatterers: 24978 At special positions: 0 Unit cell: (135.2, 142.48, 172.64, 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 111 16.00 O 4893 8.00 N 4080 7.00 C 15894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 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=2.02 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=2.04 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=9, 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 865.0 milliseconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 24.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.623A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.750A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.976A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 removed outlier: 4.037A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 755 No H-bonds generated for 'chain 'A' and resid 754 through 755' Processing helix chain 'A' and resid 756 through 757 No H-bonds generated for 'chain 'A' and resid 756 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.764A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.502A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.713A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.950A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.750A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.586A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.923A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 984 removed outlier: 3.514A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.123A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.623A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.750A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.900A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.976A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 4.037A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 755 No H-bonds generated for 'chain 'B' and resid 754 through 755' Processing helix chain 'B' and resid 756 through 757 No H-bonds generated for 'chain 'B' and resid 756 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.763A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.502A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.714A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.950A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.750A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.586A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.923A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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 984 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.123A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.624A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.751A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.900A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.976A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 removed outlier: 4.036A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 755 No H-bonds generated for 'chain 'C' and resid 754 through 755' Processing helix chain 'C' and resid 756 through 757 No H-bonds generated for 'chain 'C' and resid 756 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.764A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.502A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.714A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.951A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.750A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.586A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.922A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 984 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.122A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.557A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 7.376A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.781A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.644A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.184A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.296A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.578A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.801A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.202A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.698A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 807 through 808 removed outlier: 4.141A pdb=" N ARG A 815 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.557A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 52 removed outlier: 7.376A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.780A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.644A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.186A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.296A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.558A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.801A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.202A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD9, first strand: chain 'B' and resid 807 through 808 removed outlier: 4.141A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.558A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.376A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.780A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.644A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.185A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.295A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.801A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.202A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.578A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 807 through 808 removed outlier: 4.142A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1123 886 hydrogen bonds defined for protein. 2382 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: 6.75 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7892 1.34 - 1.46: 6297 1.46 - 1.58: 11206 1.58 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 25536 Sorted by residual: bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.06e+01 bond pdb=" N THR B 859 " pdb=" CA THR B 859 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 8.11e+00 bond pdb=" N ILE A 231 " pdb=" CA ILE A 231 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.85e+00 bond pdb=" N VAL C 860 " pdb=" CA VAL C 860 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.85e+00 ... (remaining 25531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 32468 1.65 - 3.30: 1904 3.30 - 4.96: 311 4.96 - 6.61: 48 6.61 - 8.26: 18 Bond angle restraints: 34749 Sorted by residual: angle pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta sigma weight residual 122.77 116.39 6.38 1.48e+00 4.57e-01 1.86e+01 angle pdb=" C PHE A 157 " pdb=" N ARG A 158 " pdb=" CA ARG A 158 " ideal model delta sigma weight residual 122.77 116.40 6.37 1.48e+00 4.57e-01 1.85e+01 angle pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta sigma weight residual 122.77 116.40 6.37 1.48e+00 4.57e-01 1.85e+01 angle pdb=" CA LEU C 858 " pdb=" C LEU C 858 " pdb=" O LEU C 858 " ideal model delta sigma weight residual 122.36 118.28 4.08 1.21e+00 6.83e-01 1.14e+01 angle pdb=" C ASP C 364 " pdb=" N TYR C 365 " pdb=" CA TYR C 365 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 ... (remaining 34744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 14214 17.67 - 35.33: 386 35.33 - 53.00: 70 53.00 - 70.66: 33 70.66 - 88.33: 9 Dihedral angle restraints: 14712 sinusoidal: 5706 harmonic: 9006 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.30 83.30 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.29 83.29 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.29 83.29 1 1.00e+01 1.00e-02 8.48e+01 ... (remaining 14709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 4043 0.142 - 0.284: 61 0.284 - 0.426: 2 0.426 - 0.568: 4 0.568 - 0.710: 3 Chirality restraints: 4113 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 4110 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.072 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" CG ASN A 234 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " 0.029 2.00e-02 2.50e+03 2.89e-02 1.04e+01 pdb=" CG ASN C 603 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG C1306 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.017 2.00e-02 2.50e+03 2.17e-02 5.86e+00 pdb=" CG ASN A 603 " 0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " 0.026 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 3 1.86 - 2.62: 399 2.62 - 3.38: 32988 3.38 - 4.14: 59026 4.14 - 4.90: 108970 Nonbonded interactions: 201386 Sorted by model distance: nonbonded pdb=" OH TYR C 853 " pdb=" OD1 ASN C 960 " model vdw 1.105 3.040 nonbonded pdb=" OH TYR A 853 " pdb=" OD1 ASN A 960 " model vdw 1.243 3.040 nonbonded pdb=" OH TYR B 853 " pdb=" OD1 ASN B 960 " model vdw 1.272 3.040 nonbonded pdb=" OH TYR C 853 " pdb=" CG ASN C 960 " model vdw 1.885 3.270 nonbonded pdb=" OH TYR A 853 " pdb=" CG ASN A 960 " model vdw 1.937 3.270 ... (remaining 201381 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5.570 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.080 Find NCS groups from input model: 0.620 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:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.011 0.233 25641 Z= 0.531 Angle : 0.962 22.327 35001 Z= 0.497 Chirality : 0.062 0.710 4113 Planarity : 0.005 0.045 4419 Dihedral : 9.606 88.331 8802 Min Nonbonded Distance : 1.105 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 0.82 % Allowed : 0.59 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.16 (0.12), residues: 3039 helix: -4.18 (0.11), residues: 645 sheet: -1.52 (0.15), residues: 660 loop : -1.43 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 815 TYR 0.040 0.003 TYR B 495 PHE 0.031 0.004 PHE A 497 TRP 0.021 0.003 TRP C 64 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01097 / 0.49 (25536) covalent geometry : angle 0.89280 / 0.48 (34749) SS BOND : bond 0.00637 / 0.47 ( 36) SS BOND : angle 1.41120 / 1.01 ( 72) hydrogen bonds : bond 0.27178 / 17.90 ( 877) hydrogen bonds : angle 11.75064 / 8.04 ( 2382) Misc. bond : bond 0.10377 / 5.34 ( 9) link_BETA1-4 : bond 0.01210 / 0.80 ( 15) link_BETA1-4 : angle 4.15148 / 3.10 ( 45) link_NAG-ASN : bond 0.03515 / 1.69 ( 45) link_NAG-ASN : angle 5.30545 / 4.13 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 363 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.7956 (m-30) cc_final: 0.7585 (m-30) REVERT: A 505 TYR cc_start: 0.8085 (m-10) cc_final: 0.7873 (m-80) REVERT: A 549 THR cc_start: 0.8444 (m) cc_final: 0.8186 (p) REVERT: B 420 ASP cc_start: 0.7909 (m-30) cc_final: 0.7535 (m-30) REVERT: B 505 TYR cc_start: 0.8232 (m-10) cc_final: 0.7980 (m-80) REVERT: B 549 THR cc_start: 0.8412 (m) cc_final: 0.8162 (p) REVERT: B 849 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7421 (tpt) REVERT: C 505 TYR cc_start: 0.8027 (m-10) cc_final: 0.7759 (m-80) REVERT: C 549 THR cc_start: 0.8369 (m) cc_final: 0.8133 (p) outliers start: 22 outliers final: 13 residues processed: 379 average time/residue: 0.1795 time to fit residues: 103.6519 Evaluate side-chains 164 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 854 ARG Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 437 ASN A 519 HIS A 606 ASN A 703 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1088 HIS B 66 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 519 HIS B 606 ASN B 703 ASN B 779 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 955 ASN B1011 GLN B1088 HIS C 66 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 519 HIS C 606 ASN C 703 ASN C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097812 restraints weight = 44899.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.101243 restraints weight = 24984.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103526 restraints weight = 17015.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105039 restraints weight = 13103.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106037 restraints weight = 10946.997| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25641 Z= 0.180 Angle : 0.748 15.274 35001 Z= 0.377 Chirality : 0.049 0.298 4113 Planarity : 0.005 0.044 4419 Dihedral : 6.643 58.978 3340 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.52 % Allowed : 4.76 % Favored : 93.72 % 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: -2.05 (0.13), residues: 3039 helix: -2.08 (0.16), residues: 672 sheet: -0.86 (0.17), residues: 675 loop : -1.20 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 646 TYR 0.027 0.002 TYR B 904 PHE 0.028 0.002 PHE A 643 TRP 0.016 0.002 TRP C 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (25536) covalent geometry : angle 0.68904 / 0.36 (34749) SS BOND : bond 0.00380 / 0.25 ( 36) SS BOND : angle 2.86485 / 2.05 ( 72) hydrogen bonds : bond 0.04969 / 3.19 ( 877) hydrogen bonds : angle 6.81461 / 4.68 ( 2382) Misc. bond : bond 0.00257 / 0.14 ( 9) link_BETA1-4 : bond 0.00370 / 0.25 ( 15) link_BETA1-4 : angle 1.12641 / 0.77 ( 45) link_NAG-ASN : bond 0.00509 / 0.35 ( 45) link_NAG-ASN : angle 4.24448 / 3.37 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.7810 (m-30) cc_final: 0.7022 (m-30) REVERT: A 438 SER cc_start: 0.8214 (p) cc_final: 0.7972 (p) REVERT: A 505 TYR cc_start: 0.7750 (m-80) cc_final: 0.7407 (m-80) REVERT: A 854 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7618 (mtt90) REVERT: A 922 LEU cc_start: 0.8811 (tt) cc_final: 0.8552 (mp) REVERT: B 420 ASP cc_start: 0.7711 (m-30) cc_final: 0.7348 (m-30) REVERT: B 505 TYR cc_start: 0.7817 (m-80) cc_final: 0.7445 (m-80) REVERT: B 549 THR cc_start: 0.8664 (m) cc_final: 0.8224 (p) REVERT: C 568 ASP cc_start: 0.7722 (t0) cc_final: 0.7507 (t70) REVERT: C 643 PHE cc_start: 0.7418 (t80) cc_final: 0.7169 (t80) REVERT: C 779 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7741 (tp-100) REVERT: C 900 MET cc_start: 0.7892 (ttm) cc_final: 0.7663 (mtp) outliers start: 41 outliers final: 25 residues processed: 242 average time/residue: 0.1408 time to fit residues: 56.9235 Evaluate side-chains 167 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [98, 204, 176, 247, 140, 82, 153, 242, 68, 291, 39] chunk 98 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 115 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 955 ASN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097224 restraints weight = 45551.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100618 restraints weight = 25746.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102900 restraints weight = 17671.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104393 restraints weight = 13653.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105458 restraints weight = 11425.390| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25641 Z= 0.182 Angle : 0.653 14.926 35001 Z= 0.325 Chirality : 0.047 0.278 4113 Planarity : 0.004 0.040 4419 Dihedral : 5.803 58.154 3324 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.56 % Allowed : 6.87 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 3039 helix: -0.91 (0.18), residues: 696 sheet: -0.48 (0.18), residues: 681 loop : -1.11 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 854 TYR 0.021 0.002 TYR B 495 PHE 0.020 0.002 PHE A 643 TRP 0.016 0.001 TRP C 64 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (25536) covalent geometry : angle 0.60197 / 0.31 (34749) SS BOND : bond 0.00268 / 0.17 ( 36) SS BOND : angle 1.67841 / 1.19 ( 72) hydrogen bonds : bond 0.04317 / 2.79 ( 877) hydrogen bonds : angle 6.23166 / 4.28 ( 2382) Misc. bond : bond 0.00062 / 0.04 ( 9) link_BETA1-4 : bond 0.00557 / 0.39 ( 15) link_BETA1-4 : angle 1.11086 / 0.78 ( 45) link_NAG-ASN : bond 0.00471 / 0.33 ( 45) link_NAG-ASN : angle 3.92970 / 3.14 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.7610 (m-30) cc_final: 0.7378 (m-30) REVERT: A 442 ASP cc_start: 0.8094 (m-30) cc_final: 0.7637 (m-30) REVERT: A 505 TYR cc_start: 0.7777 (m-80) cc_final: 0.7507 (m-80) REVERT: B 420 ASP cc_start: 0.7683 (m-30) cc_final: 0.7433 (m-30) REVERT: B 505 TYR cc_start: 0.7774 (m-80) cc_final: 0.7501 (m-80) REVERT: B 549 THR cc_start: 0.8637 (m) cc_final: 0.8279 (p) REVERT: C 109 THR cc_start: 0.8365 (p) cc_final: 0.8011 (t) REVERT: C 319 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7873 (mtt90) REVERT: C 568 ASP cc_start: 0.7757 (t0) cc_final: 0.7545 (t0) REVERT: C 643 PHE cc_start: 0.7410 (t80) cc_final: 0.7196 (t80) outliers start: 42 outliers final: 31 residues processed: 203 average time/residue: 0.1470 time to fit residues: 50.4748 Evaluate side-chains 169 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [25, 117, 106, 61, 19, 179, 279, 53, 62, 100, 287] chunk 25 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095643 restraints weight = 44762.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099072 restraints weight = 25086.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101361 restraints weight = 17158.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102733 restraints weight = 13238.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103849 restraints weight = 11173.229| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25641 Z= 0.193 Angle : 0.634 14.692 35001 Z= 0.314 Chirality : 0.046 0.260 4113 Planarity : 0.004 0.040 4419 Dihedral : 5.303 46.725 3312 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 6.95 % Favored : 90.93 % 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: -1.06 (0.14), residues: 3039 helix: -0.23 (0.19), residues: 687 sheet: -0.32 (0.19), residues: 660 loop : -1.03 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 854 TYR 0.017 0.001 TYR A 495 PHE 0.029 0.002 PHE B 643 TRP 0.017 0.001 TRP C 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (25536) covalent geometry : angle 0.58909 / 0.30 (34749) SS BOND : bond 0.00302 / 0.20 ( 36) SS BOND : angle 1.19273 / 0.84 ( 72) hydrogen bonds : bond 0.03944 / 2.56 ( 877) hydrogen bonds : angle 5.91835 / 4.07 ( 2382) Misc. bond : bond 0.00065 / 0.04 ( 9) link_BETA1-4 : bond 0.00416 / 0.26 ( 15) link_BETA1-4 : angle 1.08032 / 0.74 ( 45) link_NAG-ASN : bond 0.00436 / 0.30 ( 45) link_NAG-ASN : angle 3.71553 / 2.99 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.7548 (m-30) cc_final: 0.7259 (m-30) REVERT: B 549 THR cc_start: 0.8662 (m) cc_final: 0.8325 (p) REVERT: B 902 MET cc_start: 0.8612 (tpt) cc_final: 0.8233 (mmt) REVERT: C 109 THR cc_start: 0.8324 (p) cc_final: 0.8098 (t) REVERT: C 319 ARG cc_start: 0.8106 (ptp90) cc_final: 0.7888 (mtt90) REVERT: C 568 ASP cc_start: 0.7782 (t0) cc_final: 0.7539 (t0) REVERT: C 643 PHE cc_start: 0.7438 (t80) cc_final: 0.7184 (t80) outliers start: 57 outliers final: 32 residues processed: 202 average time/residue: 0.1407 time to fit residues: 48.6832 Evaluate side-chains 164 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [59, 236, 154, 281, 125, 208, 270, 141, 11, 276, 101] chunk 59 optimal weight: 0.4980 chunk 236 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 613 GLN ** C 901 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.117523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096491 restraints weight = 44649.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099923 restraints weight = 24994.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102241 restraints weight = 17061.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103784 restraints weight = 13111.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104681 restraints weight = 10935.168| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25641 Z= 0.150 Angle : 0.610 14.405 35001 Z= 0.299 Chirality : 0.045 0.248 4113 Planarity : 0.004 0.040 4419 Dihedral : 5.003 45.242 3310 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.78 % Allowed : 7.95 % Favored : 90.26 % 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: -0.80 (0.14), residues: 3039 helix: 0.18 (0.20), residues: 690 sheet: -0.17 (0.20), residues: 639 loop : -0.95 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 854 TYR 0.014 0.001 TYR B 904 PHE 0.022 0.002 PHE B 643 TRP 0.016 0.001 TRP C 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25536) covalent geometry : angle 0.56142 / 0.29 (34749) SS BOND : bond 0.00243 / 0.16 ( 36) SS BOND : angle 2.20019 / 1.53 ( 72) hydrogen bonds : bond 0.03706 / 2.40 ( 877) hydrogen bonds : angle 5.68593 / 3.92 ( 2382) Misc. bond : bond 0.00047 / 0.03 ( 9) link_BETA1-4 : bond 0.00415 / 0.27 ( 15) link_BETA1-4 : angle 1.03508 / 0.70 ( 45) link_NAG-ASN : bond 0.00441 / 0.31 ( 45) link_NAG-ASN : angle 3.51027 / 2.84 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 549 THR cc_start: 0.8630 (m) cc_final: 0.8273 (p) REVERT: C 568 ASP cc_start: 0.7721 (t0) cc_final: 0.7477 (t0) REVERT: C 643 PHE cc_start: 0.7316 (t80) cc_final: 0.7065 (t80) REVERT: C 994 ASP cc_start: 0.7963 (m-30) cc_final: 0.7584 (m-30) outliers start: 48 outliers final: 33 residues processed: 200 average time/residue: 0.1444 time to fit residues: 49.2451 Evaluate side-chains 168 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [69, 37, 134, 10, 62, 129, 68, 60, 215, 202, 269] chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 901 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 = 0.3650 r_free = 0.3650 target = 0.115871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094662 restraints weight = 44988.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098039 restraints weight = 25228.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100313 restraints weight = 17353.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101822 restraints weight = 13425.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.102775 restraints weight = 11246.286| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25641 Z= 0.211 Angle : 0.631 14.489 35001 Z= 0.310 Chirality : 0.046 0.260 4113 Planarity : 0.004 0.040 4419 Dihedral : 4.933 21.654 3306 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.82 % Allowed : 8.62 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3039 helix: 0.12 (0.20), residues: 702 sheet: -0.28 (0.20), residues: 645 loop : -0.91 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1107 TYR 0.027 0.002 TYR C 508 PHE 0.019 0.002 PHE B 643 TRP 0.015 0.001 TRP A 64 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (25536) covalent geometry : angle 0.58771 / 0.30 (34749) SS BOND : bond 0.00273 / 0.19 ( 36) SS BOND : angle 1.74193 / 1.20 ( 72) hydrogen bonds : bond 0.03727 / 2.43 ( 877) hydrogen bonds : angle 5.61668 / 3.88 ( 2382) Misc. bond : bond 0.00068 / 0.04 ( 9) link_BETA1-4 : bond 0.00418 / 0.27 ( 15) link_BETA1-4 : angle 1.06777 / 0.74 ( 45) link_NAG-ASN : bond 0.00415 / 0.28 ( 45) link_NAG-ASN : angle 3.49444 / 2.83 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 853 TYR cc_start: 0.8039 (m-10) cc_final: 0.7701 (m-10) REVERT: C 568 ASP cc_start: 0.7766 (t0) cc_final: 0.7507 (t0) REVERT: C 643 PHE cc_start: 0.7301 (t80) cc_final: 0.7023 (t80) REVERT: C 994 ASP cc_start: 0.7930 (m-30) cc_final: 0.7545 (m-30) outliers start: 49 outliers final: 33 residues processed: 180 average time/residue: 0.1445 time to fit residues: 44.5544 Evaluate side-chains 159 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [300, 57, 137, 92, 196, 282, 246, 33, 34, 124, 97] chunk 300 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 282 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096424 restraints weight = 44607.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099856 restraints weight = 24800.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102191 restraints weight = 16944.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103715 restraints weight = 12992.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104741 restraints weight = 10854.412| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25641 Z= 0.135 Angle : 0.582 14.095 35001 Z= 0.285 Chirality : 0.045 0.233 4113 Planarity : 0.003 0.040 4419 Dihedral : 4.711 20.123 3306 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.49 % Allowed : 9.96 % Favored : 88.55 % 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: -0.61 (0.15), residues: 3039 helix: 0.43 (0.20), residues: 699 sheet: -0.16 (0.20), residues: 639 loop : -0.82 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.023 0.001 TYR C 904 PHE 0.017 0.001 PHE B 643 TRP 0.016 0.001 TRP A 64 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (25536) covalent geometry : angle 0.54167 / 0.28 (34749) SS BOND : bond 0.00313 / 0.22 ( 36) SS BOND : angle 1.28425 / 0.88 ( 72) hydrogen bonds : bond 0.03501 / 2.28 ( 877) hydrogen bonds : angle 5.44588 / 3.76 ( 2382) Misc. bond : bond 0.00066 / 0.05 ( 9) link_BETA1-4 : bond 0.00412 / 0.28 ( 15) link_BETA1-4 : angle 1.01826 / 0.68 ( 45) link_NAG-ASN : bond 0.00426 / 0.30 ( 45) link_NAG-ASN : angle 3.30601 / 2.69 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: C 47 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.9061 (m) REVERT: C 568 ASP cc_start: 0.7692 (t0) cc_final: 0.7413 (t0) outliers start: 40 outliers final: 29 residues processed: 186 average time/residue: 0.1421 time to fit residues: 44.6354 Evaluate side-chains 159 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [183, 90, 85, 37, 257, 282, 61, 78, 52, 256, 180] chunk 183 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096428 restraints weight = 44484.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099882 restraints weight = 25038.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102164 restraints weight = 17045.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103690 restraints weight = 13149.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104673 restraints weight = 10979.975| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25641 Z= 0.143 Angle : 0.590 14.087 35001 Z= 0.290 Chirality : 0.045 0.231 4113 Planarity : 0.003 0.040 4419 Dihedral : 4.660 19.645 3306 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.78 % Allowed : 9.88 % Favored : 88.33 % 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: -0.53 (0.15), residues: 3039 helix: 0.52 (0.20), residues: 705 sheet: -0.17 (0.20), residues: 639 loop : -0.77 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.022 0.001 TYR C 904 PHE 0.039 0.001 PHE A 643 TRP 0.016 0.001 TRP A 64 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (25536) covalent geometry : angle 0.54982 / 0.28 (34749) SS BOND : bond 0.00532 / 0.22 ( 36) SS BOND : angle 1.65045 / 0.99 ( 72) hydrogen bonds : bond 0.03470 / 2.26 ( 877) hydrogen bonds : angle 5.36995 / 3.70 ( 2382) Misc. bond : bond 0.00058 / 0.04 ( 9) link_BETA1-4 : bond 0.00450 / 0.31 ( 15) link_BETA1-4 : angle 1.02319 / 0.69 ( 45) link_NAG-ASN : bond 0.00422 / 0.29 ( 45) link_NAG-ASN : angle 3.25493 / 2.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: A 853 TYR cc_start: 0.8009 (m-10) cc_final: 0.7648 (m-10) REVERT: B 508 TYR cc_start: 0.8709 (m-80) cc_final: 0.8462 (m-80) REVERT: C 47 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9079 (m) REVERT: C 568 ASP cc_start: 0.7684 (t0) cc_final: 0.7404 (t0) outliers start: 48 outliers final: 33 residues processed: 187 average time/residue: 0.1453 time to fit residues: 46.0374 Evaluate side-chains 167 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [18, 225, 20, 175, 228, 291, 108, 222, 79, 71, 42] chunk 18 optimal weight: 0.4980 chunk 225 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 0.0980 chunk 228 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097648 restraints weight = 44532.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101122 restraints weight = 24808.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103438 restraints weight = 16909.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104819 restraints weight = 13021.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105949 restraints weight = 10979.196| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25641 Z= 0.122 Angle : 0.574 13.798 35001 Z= 0.283 Chirality : 0.044 0.231 4113 Planarity : 0.003 0.054 4419 Dihedral : 4.532 18.483 3306 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.45 % Allowed : 10.55 % Favored : 88.00 % 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: -0.41 (0.15), residues: 3039 helix: 0.79 (0.20), residues: 690 sheet: -0.18 (0.20), residues: 630 loop : -0.73 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1091 TYR 0.014 0.001 TYR B 508 PHE 0.034 0.001 PHE A 643 TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (25536) covalent geometry : angle 0.53642 / 0.27 (34749) SS BOND : bond 0.00490 / 0.21 ( 36) SS BOND : angle 1.45397 / 0.86 ( 72) hydrogen bonds : bond 0.03387 / 2.21 ( 877) hydrogen bonds : angle 5.28199 / 3.65 ( 2382) Misc. bond : bond 0.00049 / 0.03 ( 9) link_BETA1-4 : bond 0.00410 / 0.27 ( 15) link_BETA1-4 : angle 1.02510 / 0.69 ( 45) link_NAG-ASN : bond 0.00433 / 0.30 ( 45) link_NAG-ASN : angle 3.15673 / 2.58 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 508 TYR cc_start: 0.8686 (m-80) cc_final: 0.8471 (m-80) REVERT: C 47 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9084 (m) REVERT: C 568 ASP cc_start: 0.7651 (t0) cc_final: 0.7408 (t0) outliers start: 39 outliers final: 31 residues processed: 188 average time/residue: 0.1393 time to fit residues: 44.9631 Evaluate side-chains 167 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [133, 55, 184, 93, 122, 265, 166, 86, 271, 297, 84] chunk 133 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 166 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 271 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097696 restraints weight = 44330.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101140 restraints weight = 24556.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103442 restraints weight = 16741.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104905 restraints weight = 12873.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105984 restraints weight = 10778.277| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25641 Z= 0.127 Angle : 0.608 14.083 35001 Z= 0.297 Chirality : 0.048 0.688 4113 Planarity : 0.003 0.040 4419 Dihedral : 4.558 27.795 3306 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.45 % Allowed : 10.67 % Favored : 87.89 % 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: -0.37 (0.15), residues: 3039 helix: 0.86 (0.20), residues: 690 sheet: -0.11 (0.20), residues: 627 loop : -0.73 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 646 TYR 0.019 0.001 TYR C 904 PHE 0.041 0.001 PHE C 643 TRP 0.019 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25536) covalent geometry : angle 0.55915 / 0.28 (34749) SS BOND : bond 0.00647 / 0.31 ( 36) SS BOND : angle 1.85758 / 0.98 ( 72) hydrogen bonds : bond 0.03354 / 2.18 ( 877) hydrogen bonds : angle 5.24776 / 3.63 ( 2382) Misc. bond : bond 0.00049 / 0.03 ( 9) link_BETA1-4 : bond 0.00458 / 0.32 ( 15) link_BETA1-4 : angle 1.03025 / 0.69 ( 45) link_NAG-ASN : bond 0.00561 / 0.38 ( 45) link_NAG-ASN : angle 3.63402 / 2.89 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: C 47 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.9081 (m) REVERT: C 508 TYR cc_start: 0.8653 (m-80) cc_final: 0.8451 (m-80) REVERT: C 568 ASP cc_start: 0.7692 (t0) cc_final: 0.7478 (t0) REVERT: C 1029 MET cc_start: 0.8885 (tpp) cc_final: 0.8653 (ttm) outliers start: 39 outliers final: 31 residues processed: 183 average time/residue: 0.1428 time to fit residues: 44.2597 Evaluate side-chains 171 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [108, 128, 187, 33, 157, 62, 297, 228, 156, 152, 154] chunk 108 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 297 optimal weight: 0.1980 chunk 228 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095197 restraints weight = 44700.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098568 restraints weight = 25091.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100828 restraints weight = 17247.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102325 restraints weight = 13349.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103365 restraints weight = 11193.697| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 25641 Z= 0.214 Angle : 0.666 20.564 35001 Z= 0.326 Chirality : 0.048 0.664 4113 Planarity : 0.004 0.044 4419 Dihedral : 4.758 35.768 3306 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.56 % Allowed : 10.93 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3039 helix: 0.68 (0.20), residues: 687 sheet: -0.25 (0.20), residues: 645 loop : -0.73 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 646 TYR 0.024 0.002 TYR B 508 PHE 0.039 0.002 PHE C 643 TRP 0.017 0.001 TRP A 64 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (25536) covalent geometry : angle 0.61068 / 0.31 (34749) SS BOND : bond 0.00718 / 0.34 ( 36) SS BOND : angle 2.18340 / 1.52 ( 72) hydrogen bonds : bond 0.03540 / 2.32 ( 877) hydrogen bonds : angle 5.36696 / 3.71 ( 2382) Misc. bond : bond 0.00062 / 0.04 ( 9) link_BETA1-4 : bond 0.00441 / 0.30 ( 15) link_BETA1-4 : angle 1.04721 / 0.71 ( 45) link_NAG-ASN : bond 0.00536 / 0.35 ( 45) link_NAG-ASN : angle 3.99131 / 3.27 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.43 seconds wall clock time: 63 minutes 15.17 seconds (3795.17 seconds total)