Starting phenix.real_space_refine on Sat Jul 4 14:12:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mtc_23982/07_2026/7mtc_23982.cif" } resolution = 2.6 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 91 5.16 5 C 13511 2.51 5 N 3448 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21178 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7139 Classifications: {'peptide': 914} Link IDs: {'PTRANS': 45, 'TRANS': 868} Chain breaks: 15 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6435 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 43, 'TRANS': 786} Chain breaks: 13 Chain: "C" Number of atoms: 7016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7016 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 46, 'TRANS': 851} Chain breaks: 16 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.44, per 1000 atoms: 0.26 Number of scatterers: 21178 At special positions: 0 Unit cell: (131.67, 132.525, 164.16, 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 91 16.00 O 4128 8.00 N 3448 7.00 C 13511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 331 " " 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 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 973.3 milliseconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4966 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 41 sheets defined 26.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.901A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.396A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.603A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.546A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.577A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.591A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.638A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 940 removed outlier: 4.180A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.102A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.667A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.783A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.834A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.212A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.959A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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: 3.567A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.645A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.841A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.544A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 4.021A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.516A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.916A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.666A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.713A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.164A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.001A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.866A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.612A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 279 removed outlier: 6.707A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.134A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.196A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.820A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.424A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.819A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.440A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.570A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.071A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.887A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.664A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.463A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.721A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.699A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.699A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.988A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.569A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.584A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.545A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.669A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.801A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 842 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4904 1.33 - 1.45: 5552 1.45 - 1.58: 11037 1.58 - 1.71: 0 1.71 - 1.83: 115 Bond restraints: 21608 Sorted by residual: bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.19e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CA SER B 758 " pdb=" CB SER B 758 " ideal model delta sigma weight residual 1.531 1.426 0.105 3.12e-02 1.03e+03 1.12e+01 bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.392 0.121 3.90e-02 6.57e+02 9.68e+00 bond pdb=" CB VAL B1094 " pdb=" CG1 VAL B1094 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.17e+00 ... (remaining 21603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 28965 3.55 - 7.09: 369 7.09 - 10.64: 36 10.64 - 14.19: 5 14.19 - 17.73: 1 Bond angle restraints: 29376 Sorted by residual: angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 134.30 -12.76 1.91e+00 2.74e-01 4.46e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.72 106.41 7.31 1.30e+00 5.92e-01 3.16e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.25 -6.55 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.03 -6.33 1.22e+00 6.72e-01 2.69e+01 ... (remaining 29371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 11866 16.01 - 32.02: 504 32.02 - 48.03: 130 48.03 - 64.05: 26 64.05 - 80.06: 17 Dihedral angle restraints: 12543 sinusoidal: 4877 harmonic: 7666 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.73 63.73 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA ASN B 616 " pdb=" C ASN B 616 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 12540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3364 0.143 - 0.287: 161 0.287 - 0.430: 4 0.430 - 0.573: 0 0.573 - 0.717: 2 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3528 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 823 " -0.027 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE C 823 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE C 823 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 823 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 823 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 823 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 823 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 823 " -0.022 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE A 823 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 823 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 823 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 823 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 823 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 823 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 800 " -0.026 2.00e-02 2.50e+03 2.69e-02 1.27e+01 pdb=" CG PHE A 800 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 800 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 800 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 800 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 800 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 800 " -0.007 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3284 2.76 - 3.29: 17642 3.29 - 3.83: 32646 3.83 - 4.36: 37650 4.36 - 4.90: 67458 Nonbonded interactions: 158680 Sorted by model distance: nonbonded pdb=" OE2 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.254 3.040 nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 2.305 3.120 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.338 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.354 3.040 ... (remaining 158675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 65 or resid 81 through 95 or resid 100 through \ 121 or resid 126 through 131 or resid 169 through 241 or resid 265 through 343 o \ r resid 358 through 368 or resid 383 through 395 or resid 399 through 400 or res \ id 492 or resid 521 through 620 or resid 641 through 675 or resid 690 through 82 \ 6 or resid 855 through 940 or resid 943 through 1143 or resid 1301 through 1304) \ ) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 109 or resid 115 throug \ h 172 or resid 189 through 209 or resid 216 through 241 or resid 265 through 395 \ or resid 514 through 515 or resid 518 or resid 521 through 620 or resid 641 thr \ ough 675 or resid 690 through 940 or resid 943 through 1143 or resid 1302 throug \ h 1305)) selection = (chain 'C' and (resid 27 through 65 or resid 81 through 130 or resid 166 or resi \ d 169 through 172 or resid 189 through 241 or resid 265 through 343 or resid 358 \ through 368 or resid 383 through 395 or resid 399 through 400 or resid 492 or r \ esid 521 through 620 or resid 641 through 826 or resid 855 through 1143 or resid \ 1301 through 1304)) } 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.470 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 : 0.013 0.121 21679 Z= 0.544 Angle : 1.159 17.735 29560 Z= 0.624 Chirality : 0.076 0.717 3531 Planarity : 0.009 0.077 3708 Dihedral : 10.669 80.057 7490 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.56 % Allowed : 2.33 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.14), residues: 2548 helix: -1.38 (0.17), residues: 628 sheet: -0.67 (0.21), residues: 566 loop : -2.76 (0.13), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A1019 TYR 0.043 0.005 TYR B 279 PHE 0.065 0.006 PHE C 823 TRP 0.049 0.006 TRP A 886 HIS 0.019 0.005 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01341 / 0.54 (21608) covalent geometry : angle 1.13514 / 0.62 (29376) SS BOND : bond 0.00657 / 0.35 ( 29) SS BOND : angle 3.10675 / 1.97 ( 58) hydrogen bonds : bond 0.20812 / 13.12 ( 806) hydrogen bonds : angle 7.36357 / 5.01 ( 2337) link_BETA1-4 : bond 0.00933 / 0.58 ( 14) link_BETA1-4 : angle 2.56440 / 1.59 ( 42) link_NAG-ASN : bond 0.00672 / 0.42 ( 28) link_NAG-ASN : angle 3.49728 / 2.04 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 809 PRO cc_start: 0.7746 (Cg_endo) cc_final: 0.7177 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8192 (mp0) cc_final: 0.7945 (mp0) REVERT: C 239 GLN cc_start: 0.8064 (pt0) cc_final: 0.7585 (pt0) outliers start: 13 outliers final: 3 residues processed: 292 average time/residue: 0.6354 time to fit residues: 210.7221 Evaluate side-chains 151 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 370 ASN A 414 GLN A 901 GLN A 957 GLN A1010 GLN B 207 HIS B 540 ASN B 606 ASN B 762 GLN B 804 GLN B 901 GLN B 935 GLN B 957 GLN B1002 GLN C 354 ASN C 370 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083040 restraints weight = 30118.434| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.26 r_work: 0.2848 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21679 Z= 0.142 Angle : 0.667 15.340 29560 Z= 0.336 Chirality : 0.047 0.278 3531 Planarity : 0.005 0.049 3708 Dihedral : 5.397 59.758 2788 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.90 % Allowed : 6.81 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.15), residues: 2548 helix: 0.45 (0.21), residues: 630 sheet: 0.11 (0.20), residues: 595 loop : -2.28 (0.14), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.026 0.002 TYR B 904 PHE 0.019 0.002 PHE C 32 TRP 0.018 0.002 TRP B 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21608) covalent geometry : angle 0.64733 / 0.33 (29376) SS BOND : bond 0.00256 / 0.17 ( 29) SS BOND : angle 1.35896 / 0.81 ( 58) hydrogen bonds : bond 0.06521 / 4.15 ( 806) hydrogen bonds : angle 5.58463 / 3.79 ( 2337) link_BETA1-4 : bond 0.00402 / 0.26 ( 14) link_BETA1-4 : angle 1.28015 / 0.81 ( 42) link_NAG-ASN : bond 0.00488 / 0.30 ( 28) link_NAG-ASN : angle 2.78778 / 1.61 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7161 (mmp-170) cc_final: 0.6914 (mmt90) REVERT: A 200 TYR cc_start: 0.7408 (m-80) cc_final: 0.6866 (m-80) REVERT: A 281 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: A 347 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4301 (m-80) REVERT: A 529 LYS cc_start: 0.8371 (mppt) cc_final: 0.8018 (mmmt) REVERT: A 556 ASN cc_start: 0.7794 (t0) cc_final: 0.7562 (t0) REVERT: A 646 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8046 (mtm110) REVERT: A 654 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 740 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8499 (ttt) REVERT: A 1005 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8890 (mt0) REVERT: B 102 ARG cc_start: 0.7758 (mmm160) cc_final: 0.6930 (mmm-85) REVERT: B 271 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: B 314 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: B 529 LYS cc_start: 0.8299 (mmtm) cc_final: 0.7961 (mtpp) REVERT: B 809 PRO cc_start: 0.7590 (Cg_endo) cc_final: 0.7020 (Cg_exo) REVERT: B 904 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6685 (p90) REVERT: B 988 GLU cc_start: 0.8656 (mp0) cc_final: 0.8124 (mp0) REVERT: C 33 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7481 (p) REVERT: C 239 GLN cc_start: 0.8070 (pt0) cc_final: 0.7591 (pt0) REVERT: C 560 LEU cc_start: 0.8129 (mt) cc_final: 0.7650 (mp) REVERT: C 1092 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7875 (pm20) outliers start: 44 outliers final: 9 residues processed: 213 average time/residue: 0.6032 time to fit residues: 146.8876 Evaluate side-chains 166 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 16 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 23 optimal weight: 0.1980 chunk 163 optimal weight: 0.0980 chunk 174 optimal weight: 10.0000 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS B 957 GLN B1002 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083718 restraints weight = 30175.153| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.25 r_work: 0.2881 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 21679 Z= 0.111 Angle : 0.600 13.890 29560 Z= 0.298 Chirality : 0.045 0.260 3531 Planarity : 0.004 0.049 3708 Dihedral : 4.835 57.299 2787 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.85 % Allowed : 8.19 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2548 helix: 1.20 (0.22), residues: 629 sheet: 0.33 (0.21), residues: 594 loop : -1.93 (0.15), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.019 0.001 TYR B 904 PHE 0.018 0.001 PHE A 32 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (21608) covalent geometry : angle 0.57940 / 0.29 (29376) SS BOND : bond 0.00274 / 0.20 ( 29) SS BOND : angle 1.31374 / 0.80 ( 58) hydrogen bonds : bond 0.05234 / 3.34 ( 806) hydrogen bonds : angle 5.14771 / 3.50 ( 2337) link_BETA1-4 : bond 0.00440 / 0.28 ( 14) link_BETA1-4 : angle 1.14554 / 0.73 ( 42) link_NAG-ASN : bond 0.00426 / 0.24 ( 28) link_NAG-ASN : angle 2.74561 / 1.58 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7433 (m-80) cc_final: 0.6856 (m-80) REVERT: A 281 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: A 347 PHE cc_start: 0.5106 (OUTLIER) cc_final: 0.4494 (m-80) REVERT: A 428 ASP cc_start: 0.7838 (p0) cc_final: 0.7622 (p0) REVERT: A 529 LYS cc_start: 0.8365 (mppt) cc_final: 0.8049 (mmmt) REVERT: A 556 ASN cc_start: 0.7822 (t0) cc_final: 0.7537 (t0) REVERT: A 646 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8029 (ttp80) REVERT: A 654 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 740 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: A 790 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8587 (mtmt) REVERT: A 1005 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8823 (mt0) REVERT: B 102 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7475 (mmm-85) REVERT: B 271 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: B 529 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7819 (mtpp) REVERT: B 581 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7723 (p) REVERT: B 809 PRO cc_start: 0.7483 (Cg_endo) cc_final: 0.6992 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8632 (mp0) cc_final: 0.8080 (mp0) REVERT: C 33 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7453 (p) REVERT: C 239 GLN cc_start: 0.8028 (pt0) cc_final: 0.7656 (pt0) REVERT: C 560 LEU cc_start: 0.8053 (mt) cc_final: 0.7557 (mp) REVERT: C 1092 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7793 (pm20) outliers start: 43 outliers final: 10 residues processed: 192 average time/residue: 0.5506 time to fit residues: 122.7661 Evaluate side-chains 162 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 231 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 207 HIS B 957 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082214 restraints weight = 30065.385| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.27 r_work: 0.2832 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21679 Z= 0.139 Angle : 0.623 14.334 29560 Z= 0.311 Chirality : 0.046 0.261 3531 Planarity : 0.004 0.044 3708 Dihedral : 4.779 54.354 2787 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.59 % Allowed : 8.32 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2548 helix: 1.42 (0.22), residues: 636 sheet: 0.53 (0.21), residues: 599 loop : -1.79 (0.15), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.023 0.001 TYR B1067 PHE 0.019 0.002 PHE C 32 TRP 0.008 0.001 TRP A 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21608) covalent geometry : angle 0.60431 / 0.31 (29376) SS BOND : bond 0.00307 / 0.20 ( 29) SS BOND : angle 1.46883 / 0.89 ( 58) hydrogen bonds : bond 0.06153 / 3.93 ( 806) hydrogen bonds : angle 5.07306 / 3.44 ( 2337) link_BETA1-4 : bond 0.00380 / 0.25 ( 14) link_BETA1-4 : angle 1.14173 / 0.72 ( 42) link_NAG-ASN : bond 0.00465 / 0.26 ( 28) link_NAG-ASN : angle 2.60334 / 1.48 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 157 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6780 (mmt90) REVERT: A 200 TYR cc_start: 0.7492 (m-80) cc_final: 0.6827 (m-80) REVERT: A 281 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: A 304 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8268 (mttm) REVERT: A 347 PHE cc_start: 0.5111 (OUTLIER) cc_final: 0.4527 (m-80) REVERT: A 529 LYS cc_start: 0.8402 (mppt) cc_final: 0.8096 (mmmt) REVERT: A 556 ASN cc_start: 0.7802 (t0) cc_final: 0.7495 (t0) REVERT: A 646 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: A 654 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: A 740 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8543 (ttt) REVERT: B 271 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: B 314 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: B 529 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7802 (mtpp) REVERT: B 581 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 809 PRO cc_start: 0.7358 (Cg_endo) cc_final: 0.6892 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8671 (mp0) cc_final: 0.8105 (mp0) REVERT: C 33 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7457 (p) REVERT: C 239 GLN cc_start: 0.8028 (pt0) cc_final: 0.7684 (tt0) REVERT: C 560 LEU cc_start: 0.8054 (mt) cc_final: 0.7555 (mp) REVERT: C 855 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: C 1092 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (pm20) outliers start: 60 outliers final: 18 residues processed: 199 average time/residue: 0.5696 time to fit residues: 131.0488 Evaluate side-chains 177 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 200 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 207 HIS B 935 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082186 restraints weight = 29789.552| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.23 r_work: 0.2831 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21679 Z= 0.142 Angle : 0.617 14.599 29560 Z= 0.309 Chirality : 0.046 0.351 3531 Planarity : 0.004 0.043 3708 Dihedral : 4.711 53.551 2787 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.33 % Allowed : 9.06 % Favored : 88.62 % 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: -0.39 (0.16), residues: 2548 helix: 1.53 (0.22), residues: 636 sheet: 0.62 (0.21), residues: 610 loop : -1.70 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.025 0.001 TYR A 170 PHE 0.019 0.001 PHE C 32 TRP 0.007 0.001 TRP A 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (21608) covalent geometry : angle 0.60048 / 0.30 (29376) SS BOND : bond 0.00299 / 0.20 ( 29) SS BOND : angle 1.35478 / 0.84 ( 58) hydrogen bonds : bond 0.06129 / 3.92 ( 806) hydrogen bonds : angle 5.00554 / 3.39 ( 2337) link_BETA1-4 : bond 0.00352 / 0.23 ( 14) link_BETA1-4 : angle 1.11899 / 0.71 ( 42) link_NAG-ASN : bond 0.00454 / 0.24 ( 28) link_NAG-ASN : angle 2.48251 / 1.40 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7291 (mmp-170) cc_final: 0.6782 (mmt90) REVERT: A 200 TYR cc_start: 0.7455 (m-80) cc_final: 0.6772 (m-80) REVERT: A 281 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: A 304 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8259 (mttm) REVERT: A 347 PHE cc_start: 0.5068 (OUTLIER) cc_final: 0.4633 (m-80) REVERT: A 428 ASP cc_start: 0.7776 (p0) cc_final: 0.7576 (p0) REVERT: A 462 LYS cc_start: 0.8831 (mppt) cc_final: 0.8588 (mppt) REVERT: A 529 LYS cc_start: 0.8399 (mppt) cc_final: 0.8102 (mmmt) REVERT: A 556 ASN cc_start: 0.7812 (t0) cc_final: 0.7480 (t0) REVERT: A 646 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8042 (ttp80) REVERT: A 654 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: A 740 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8232 (ttp) REVERT: B 102 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: B 271 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: B 314 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: B 529 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7794 (mtpp) REVERT: B 581 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7650 (p) REVERT: B 809 PRO cc_start: 0.7232 (Cg_endo) cc_final: 0.6830 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8668 (mp0) cc_final: 0.8121 (mp0) REVERT: C 33 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 560 LEU cc_start: 0.8007 (mt) cc_final: 0.7509 (mp) REVERT: C 855 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: C 1092 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7893 (pm20) outliers start: 54 outliers final: 19 residues processed: 198 average time/residue: 0.5295 time to fit residues: 122.5424 Evaluate side-chains 177 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 224 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 246 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 957 GLN B 121 ASN B 207 HIS B 804 GLN B 935 GLN B1002 GLN C 354 ASN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079404 restraints weight = 29895.406| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.25 r_work: 0.2784 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21679 Z= 0.236 Angle : 0.709 15.615 29560 Z= 0.360 Chirality : 0.051 0.404 3531 Planarity : 0.005 0.041 3708 Dihedral : 5.018 53.508 2787 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.63 % Allowed : 9.36 % Favored : 88.01 % 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: -0.56 (0.16), residues: 2548 helix: 1.32 (0.21), residues: 630 sheet: 0.61 (0.21), residues: 597 loop : -1.78 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 190 TYR 0.030 0.002 TYR B 904 PHE 0.022 0.002 PHE C 32 TRP 0.008 0.002 TRP A 886 HIS 0.008 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 (21608) covalent geometry : angle 0.69077 / 0.36 (29376) SS BOND : bond 0.00425 / 0.25 ( 29) SS BOND : angle 1.72671 / 1.08 ( 58) hydrogen bonds : bond 0.07814 / 5.00 ( 806) hydrogen bonds : angle 5.23370 / 3.54 ( 2337) link_BETA1-4 : bond 0.00342 / 0.23 ( 14) link_BETA1-4 : angle 1.32368 / 0.83 ( 42) link_NAG-ASN : bond 0.00509 / 0.28 ( 28) link_NAG-ASN : angle 2.65071 / 1.52 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7371 (mmp-170) cc_final: 0.6876 (mmt90) REVERT: A 200 TYR cc_start: 0.7503 (m-80) cc_final: 0.6737 (m-80) REVERT: A 281 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7226 (pp20) REVERT: A 304 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8299 (mttm) REVERT: A 462 LYS cc_start: 0.8814 (mppt) cc_final: 0.8586 (mppt) REVERT: A 529 LYS cc_start: 0.8453 (mppt) cc_final: 0.8134 (mmmt) REVERT: A 556 ASN cc_start: 0.7828 (t0) cc_final: 0.7484 (t0) REVERT: A 646 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8120 (ttp80) REVERT: A 654 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 740 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8485 (ttt) REVERT: B 102 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.7466 (mmm-85) REVERT: B 271 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: B 314 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: B 529 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7789 (mtpp) REVERT: B 581 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7573 (p) REVERT: B 809 PRO cc_start: 0.7260 (Cg_endo) cc_final: 0.6860 (Cg_exo) REVERT: B 904 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6644 (p90) REVERT: B 988 GLU cc_start: 0.8705 (mp0) cc_final: 0.8411 (mp0) REVERT: C 560 LEU cc_start: 0.8057 (mt) cc_final: 0.7574 (mp) REVERT: C 855 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6957 (m-80) outliers start: 61 outliers final: 30 residues processed: 196 average time/residue: 0.5432 time to fit residues: 123.7566 Evaluate side-chains 187 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 173 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 203 optimal weight: 30.0000 chunk 60 optimal weight: 0.0770 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 957 GLN B1002 GLN C 354 ASN C 556 ASN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082132 restraints weight = 29753.712| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.22 r_work: 0.2834 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21679 Z= 0.131 Angle : 0.616 14.162 29560 Z= 0.308 Chirality : 0.046 0.357 3531 Planarity : 0.004 0.040 3708 Dihedral : 4.699 53.338 2787 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.81 % Allowed : 10.31 % Favored : 87.88 % 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: -0.28 (0.16), residues: 2548 helix: 1.61 (0.22), residues: 629 sheet: 0.81 (0.21), residues: 593 loop : -1.65 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.026 0.001 TYR A 170 PHE 0.019 0.001 PHE A 32 TRP 0.008 0.001 TRP B 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21608) covalent geometry : angle 0.59846 / 0.30 (29376) SS BOND : bond 0.00277 / 0.19 ( 29) SS BOND : angle 1.41685 / 0.85 ( 58) hydrogen bonds : bond 0.05898 / 3.77 ( 806) hydrogen bonds : angle 4.96831 / 3.37 ( 2337) link_BETA1-4 : bond 0.00383 / 0.25 ( 14) link_BETA1-4 : angle 1.10158 / 0.71 ( 42) link_NAG-ASN : bond 0.00447 / 0.24 ( 28) link_NAG-ASN : angle 2.51690 / 1.41 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7333 (mmp-170) cc_final: 0.6809 (mmt90) REVERT: A 281 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: A 304 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8277 (mttm) REVERT: A 347 PHE cc_start: 0.5045 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: A 462 LYS cc_start: 0.8838 (mppt) cc_final: 0.8573 (mppt) REVERT: A 529 LYS cc_start: 0.8370 (mppt) cc_final: 0.8047 (mmmt) REVERT: A 556 ASN cc_start: 0.7758 (t0) cc_final: 0.7398 (t0) REVERT: A 646 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8045 (ttp80) REVERT: A 654 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: A 740 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8188 (ttp) REVERT: B 102 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.7298 (mmm-85) REVERT: B 271 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: B 314 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: B 529 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7812 (mtpp) REVERT: B 581 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7649 (p) REVERT: B 809 PRO cc_start: 0.7152 (Cg_endo) cc_final: 0.6781 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8666 (mp0) cc_final: 0.8136 (mp0) REVERT: C 560 LEU cc_start: 0.7997 (mt) cc_final: 0.7501 (mp) REVERT: C 794 ILE cc_start: 0.7949 (mm) cc_final: 0.7375 (pp) REVERT: C 855 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.6928 (m-80) outliers start: 42 outliers final: 17 residues processed: 188 average time/residue: 0.5183 time to fit residues: 113.4347 Evaluate side-chains 167 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 260 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 145 optimal weight: 0.0870 chunk 104 optimal weight: 5.9990 chunk 195 optimal weight: 0.1980 chunk 221 optimal weight: 4.9990 chunk 233 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 957 GLN B 207 HIS B1002 GLN C 354 ASN C 556 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083783 restraints weight = 29908.000| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.22 r_work: 0.2866 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21679 Z= 0.112 Angle : 0.593 16.034 29560 Z= 0.295 Chirality : 0.045 0.328 3531 Planarity : 0.004 0.040 3708 Dihedral : 4.481 52.271 2787 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.72 % Allowed : 10.82 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2548 helix: 1.78 (0.22), residues: 636 sheet: 0.84 (0.21), residues: 614 loop : -1.54 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.024 0.001 TYR A 453 PHE 0.022 0.001 PHE C 168 TRP 0.008 0.001 TRP B 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (21608) covalent geometry : angle 0.57599 / 0.29 (29376) SS BOND : bond 0.00254 / 0.18 ( 29) SS BOND : angle 1.42251 / 0.92 ( 58) hydrogen bonds : bond 0.05109 / 3.27 ( 806) hydrogen bonds : angle 4.80593 / 3.26 ( 2337) link_BETA1-4 : bond 0.00405 / 0.26 ( 14) link_BETA1-4 : angle 1.03032 / 0.67 ( 42) link_NAG-ASN : bond 0.00462 / 0.24 ( 28) link_NAG-ASN : angle 2.41090 / 1.33 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: A 304 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8284 (mttm) REVERT: A 347 PHE cc_start: 0.5195 (OUTLIER) cc_final: 0.4905 (m-80) REVERT: A 462 LYS cc_start: 0.8841 (mppt) cc_final: 0.8493 (mppt) REVERT: A 529 LYS cc_start: 0.8379 (mppt) cc_final: 0.8051 (mmmt) REVERT: A 556 ASN cc_start: 0.7738 (t0) cc_final: 0.7369 (t0) REVERT: A 646 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7984 (ttp80) REVERT: A 654 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: A 740 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8172 (ttp) REVERT: B 102 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7262 (mmm-85) REVERT: B 314 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: B 529 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7803 (mtpp) REVERT: B 581 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7667 (p) REVERT: B 809 PRO cc_start: 0.7092 (Cg_endo) cc_final: 0.6717 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8654 (mp0) cc_final: 0.8088 (mp0) REVERT: C 556 ASN cc_start: 0.8270 (m-40) cc_final: 0.8024 (m-40) REVERT: C 560 LEU cc_start: 0.7991 (mt) cc_final: 0.7519 (mp) REVERT: C 794 ILE cc_start: 0.7898 (mm) cc_final: 0.7327 (pp) REVERT: C 855 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: C 1092 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7878 (pm20) outliers start: 40 outliers final: 15 residues processed: 174 average time/residue: 0.4781 time to fit residues: 97.9211 Evaluate side-chains 162 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 210 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A 414 GLN A 532 ASN A 957 GLN B1002 GLN C 207 HIS C 354 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079908 restraints weight = 29838.917| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.24 r_work: 0.2795 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 21679 Z= 0.214 Angle : 0.687 16.000 29560 Z= 0.348 Chirality : 0.050 0.334 3531 Planarity : 0.005 0.040 3708 Dihedral : 4.902 52.831 2787 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.11 % Allowed : 10.56 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.32 (0.16), residues: 2548 helix: 1.53 (0.21), residues: 629 sheet: 0.75 (0.21), residues: 605 loop : -1.65 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.031 0.002 TYR B 904 PHE 0.023 0.002 PHE C 32 TRP 0.007 0.002 TRP B 886 HIS 0.009 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.21 (21608) covalent geometry : angle 0.66631 / 0.34 (29376) SS BOND : bond 0.00464 / 0.32 ( 29) SS BOND : angle 2.18611 / 1.46 ( 58) hydrogen bonds : bond 0.07438 / 4.76 ( 806) hydrogen bonds : angle 5.12490 / 3.47 ( 2337) link_BETA1-4 : bond 0.00340 / 0.23 ( 14) link_BETA1-4 : angle 1.23902 / 0.78 ( 42) link_NAG-ASN : bond 0.00489 / 0.26 ( 28) link_NAG-ASN : angle 2.59213 / 1.47 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7459 (m-80) cc_final: 0.6526 (m-80) REVERT: A 281 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7243 (pp20) REVERT: A 304 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8343 (mttm) REVERT: A 462 LYS cc_start: 0.8826 (mppt) cc_final: 0.8503 (mppt) REVERT: A 529 LYS cc_start: 0.8413 (mppt) cc_final: 0.8074 (mmmt) REVERT: A 556 ASN cc_start: 0.7784 (t0) cc_final: 0.7428 (t0) REVERT: A 646 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8074 (ttp80) REVERT: A 654 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: A 740 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8471 (ttt) REVERT: B 102 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7296 (mmm-85) REVERT: B 314 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: B 529 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7831 (mtpp) REVERT: B 581 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7577 (p) REVERT: B 809 PRO cc_start: 0.7117 (Cg_endo) cc_final: 0.6737 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8704 (mp0) cc_final: 0.8389 (mp0) REVERT: C 556 ASN cc_start: 0.8290 (m-40) cc_final: 0.8033 (m-40) REVERT: C 560 LEU cc_start: 0.8021 (mt) cc_final: 0.7515 (mp) REVERT: C 794 ILE cc_start: 0.8060 (mm) cc_final: 0.7505 (pp) REVERT: C 855 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6923 (m-80) outliers start: 49 outliers final: 27 residues processed: 177 average time/residue: 0.4602 time to fit residues: 95.6767 Evaluate side-chains 173 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 147 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN B 207 HIS B1002 GLN C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083289 restraints weight = 30025.902| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.25 r_work: 0.2853 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21679 Z= 0.119 Angle : 0.599 15.483 29560 Z= 0.299 Chirality : 0.045 0.306 3531 Planarity : 0.004 0.041 3708 Dihedral : 4.559 52.521 2787 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.38 % Allowed : 11.25 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.13 (0.16), residues: 2548 helix: 1.69 (0.21), residues: 635 sheet: 0.89 (0.21), residues: 618 loop : -1.59 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.023 0.001 TYR A 170 PHE 0.019 0.001 PHE C 168 TRP 0.008 0.001 TRP B 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (21608) covalent geometry : angle 0.58232 / 0.30 (29376) SS BOND : bond 0.00322 / 0.24 ( 29) SS BOND : angle 1.37941 / 0.89 ( 58) hydrogen bonds : bond 0.05303 / 3.38 ( 806) hydrogen bonds : angle 4.83678 / 3.27 ( 2337) link_BETA1-4 : bond 0.00373 / 0.24 ( 14) link_BETA1-4 : angle 1.03410 / 0.67 ( 42) link_NAG-ASN : bond 0.00403 / 0.21 ( 28) link_NAG-ASN : angle 2.42692 / 1.35 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7244 (mmp-170) cc_final: 0.6936 (mmp80) REVERT: A 200 TYR cc_start: 0.7463 (m-80) cc_final: 0.6571 (m-80) REVERT: A 281 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7435 (pp20) REVERT: A 304 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8288 (mttm) REVERT: A 462 LYS cc_start: 0.8831 (mppt) cc_final: 0.8511 (mppt) REVERT: A 529 LYS cc_start: 0.8391 (mppt) cc_final: 0.8050 (mmmt) REVERT: A 556 ASN cc_start: 0.7761 (t0) cc_final: 0.7402 (t0) REVERT: A 646 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7997 (ttp80) REVERT: A 654 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: A 740 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8177 (ttp) REVERT: B 102 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7190 (mmm-85) REVERT: B 314 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: B 529 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7810 (mtpp) REVERT: B 581 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7586 (p) REVERT: B 809 PRO cc_start: 0.7049 (Cg_endo) cc_final: 0.6657 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8680 (mp0) cc_final: 0.8140 (mp0) REVERT: C 516 GLU cc_start: 0.7045 (pm20) cc_final: 0.6648 (pp20) REVERT: C 556 ASN cc_start: 0.8303 (m-40) cc_final: 0.8031 (m-40) REVERT: C 560 LEU cc_start: 0.7985 (mt) cc_final: 0.7506 (mp) REVERT: C 794 ILE cc_start: 0.7909 (mm) cc_final: 0.7374 (pp) REVERT: C 855 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6886 (m-80) outliers start: 32 outliers final: 16 residues processed: 162 average time/residue: 0.5438 time to fit residues: 101.8976 Evaluate side-chains 159 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 220 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.080648 restraints weight = 30000.847| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.25 r_work: 0.2806 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21679 Z= 0.178 Angle : 0.657 16.801 29560 Z= 0.331 Chirality : 0.048 0.320 3531 Planarity : 0.004 0.040 3708 Dihedral : 4.759 52.756 2787 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.94 % Allowed : 11.00 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.19 (0.16), residues: 2548 helix: 1.67 (0.21), residues: 629 sheet: 0.73 (0.21), residues: 624 loop : -1.56 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.027 0.002 TYR B 904 PHE 0.022 0.002 PHE C 32 TRP 0.008 0.001 TRP C 64 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (21608) covalent geometry : angle 0.63938 / 0.33 (29376) SS BOND : bond 0.00395 / 0.27 ( 29) SS BOND : angle 1.72569 / 1.12 ( 58) hydrogen bonds : bond 0.06801 / 4.35 ( 806) hydrogen bonds : angle 5.01873 / 3.39 ( 2337) link_BETA1-4 : bond 0.00353 / 0.23 ( 14) link_BETA1-4 : angle 1.15323 / 0.74 ( 42) link_NAG-ASN : bond 0.00452 / 0.24 ( 28) link_NAG-ASN : angle 2.50613 / 1.41 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8294.39 seconds wall clock time: 141 minutes 46.31 seconds (8506.31 seconds total)