Starting phenix.real_space_refine on Sun Sep 13 11:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xkl_22221/09_2026/6xkl_22221.map" } resolution = 3.21 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= 0.001 sd= 0.063 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 101 5.16 5 C 14591 2.51 5 N 3730 2.21 5 O 4473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22895 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7447 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 53, 'TRANS': 922} Chain breaks: 12 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'TYR:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "C" Number of atoms: 7355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7355 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 52, 'TRANS': 923} Chain breaks: 12 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 205 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.38, per 1000 atoms: 0.23 Number of scatterers: 22895 At special positions: 0 Unit cell: (131.76, 132.84, 186.84, 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 101 16.00 O 4473 8.00 N 3730 7.00 C 14591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5496 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 41 sheets defined 26.4% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.824A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.693A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.385A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.715A 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: 3.627A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.678A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.515A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.557A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.152A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.761A 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 976 through 984 removed outlier: 3.542A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.933A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.879A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.530A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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 758 through 783 removed outlier: 4.166A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.609A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.713A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.531A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.532A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.284A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.606A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.800A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.385A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.876A 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 758 through 783 removed outlier: 3.722A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.649A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.403A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.010A 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 982 removed outlier: 3.525A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.536A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.742A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.959A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.025A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.967A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.436A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.456A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.096A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.511A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.840A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.750A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.953A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.955A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.534A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.062A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.313A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.675A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.461A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.529A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.529A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.487A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.779A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.556A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.998A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.078A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.566A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.140A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.287A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.674A 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: 3.615A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.615A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.672A 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: 4.412A 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 1125 removed outlier: 4.613A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 969 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7270 1.34 - 1.47: 6157 1.47 - 1.60: 9830 1.60 - 1.73: 0 1.73 - 1.86: 125 Bond restraints: 23382 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" CB ASN B1074 " pdb=" CG ASN B1074 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.63e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" CB THR A1077 " pdb=" CG2 THR A1077 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.33e+00 bond pdb=" CB GLU C 819 " pdb=" CG GLU C 819 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.16e+00 ... (remaining 23377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 31729 4.51 - 9.02: 146 9.02 - 13.54: 6 13.54 - 18.05: 1 18.05 - 22.56: 1 Bond angle restraints: 31883 Sorted by residual: angle pdb=" C ASN B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta sigma weight residual 122.20 144.76 -22.56 3.42e+00 8.55e-02 4.35e+01 angle pdb=" C ASN A 30 " pdb=" N SER A 31 " pdb=" CA SER A 31 " ideal model delta sigma weight residual 121.18 131.13 -9.95 1.98e+00 2.55e-01 2.52e+01 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 angle pdb=" C GLN A 613 " pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 121.53 114.19 7.34 1.53e+00 4.27e-01 2.30e+01 angle pdb=" CA GLU A1031 " pdb=" CB GLU A1031 " pdb=" CG GLU A1031 " ideal model delta sigma weight residual 114.10 122.77 -8.67 2.00e+00 2.50e-01 1.88e+01 ... (remaining 31878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12224 17.98 - 35.97: 1015 35.97 - 53.95: 189 53.95 - 71.93: 56 71.93 - 89.91: 27 Dihedral angle restraints: 13511 sinusoidal: 5017 harmonic: 8494 Sorted by residual: dihedral pdb=" CA GLN B 173 " pdb=" C GLN B 173 " pdb=" N PRO B 174 " pdb=" CA PRO B 174 " ideal model delta harmonic sigma weight residual -180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CD ARG B 567 " pdb=" NE ARG B 567 " pdb=" CZ ARG B 567 " pdb=" NH1 ARG B 567 " ideal model delta sinusoidal sigma weight residual 0.00 37.32 -37.32 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " pdb=" NH1 ARG A 983 " ideal model delta sinusoidal sigma weight residual 0.00 -34.02 34.02 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 13508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 3850 0.235 - 0.470: 4 0.470 - 0.705: 1 0.705 - 0.940: 1 0.940 - 1.175: 1 Chirality restraints: 3857 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.45e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 3854 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 567 " -0.227 9.50e-02 1.11e+02 1.26e-01 7.67e+01 pdb=" NE ARG B 567 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 567 " -0.142 2.00e-02 2.50e+03 pdb=" NH1 ARG B 567 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 567 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.211 9.50e-02 1.11e+02 1.16e-01 6.30e+01 pdb=" NE ARG A 983 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " -0.129 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1039 " 0.128 9.50e-02 1.11e+02 7.44e-02 2.99e+01 pdb=" NE ARG B1039 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B1039 " 0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG B1039 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG B1039 " -0.025 2.00e-02 2.50e+03 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 216 2.61 - 3.18: 19330 3.18 - 3.75: 31706 3.75 - 4.33: 43730 4.33 - 4.90: 74888 Nonbonded interactions: 169870 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.034 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASN C 439 " pdb=" OG SER C 443 " model vdw 2.177 3.040 ... (remaining 169865 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 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 344 or (resid 345 through 346 and (name N or name CA or na \ me C or name O or name CB )) or resid 347 through 350 or (resid 351 through 352 \ and (name N or name CA or name C or name O or name CB )) or resid 353 through 36 \ 3 or (resid 364 and (name N or name CA or name C or name O or name CB )) or resi \ d 365 through 368 or (resid 369 and (name N or name CA or name C or name O or na \ me CB )) or resid 370 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 407 or (resid 408 and (name N or n \ ame CA or name C or name O or name CB )) or resid 409 through 441 or (resid 442 \ and (name N or name CA or name C or name O or name CB )) or resid 443 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 496 or (resid 497 through 498 and (name N or name CA or name C or name O or na \ me CB )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 508 or (resid 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 620 or resid 641 t \ hrough 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 333 or (resid 334 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 through 348 or (resid 34 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 350 or (resi \ d 351 through 352 and (name N or name CA or name C or name O or name CB )) or re \ sid 353 through 363 or (resid 364 and (name N or name CA or name C or name O or \ name CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name \ C or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 through 426 or (resid 42 \ 7 through 428 and (name N or name CA or name C or name O or name CB )) or resid \ 429 through 441 or (resid 442 and (name N or name CA or name C or name O or name \ CB )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name \ N or name CA or name C or name O or name CB )) or resid 494 through 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 508 or (resid 509 and (name N or name CA or name C or name O or \ name CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 th \ rough 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 344 or (r \ esid 345 through 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 454 or resid 491 through 504 or (resid 505 and (name N or nam \ e CA or name C or name O or name CB )) or resid 506 through 1307)) } 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' } 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: 7.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.370 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.009 0.074 23468 Z= 0.354 Angle : 1.104 22.561 32105 Z= 0.593 Chirality : 0.067 1.175 3857 Planarity : 0.008 0.126 4055 Dihedral : 14.449 89.914 7907 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.78 % Rotamer: Outliers : 3.62 % Allowed : 9.69 % Favored : 86.69 % 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: -0.34 (0.14), residues: 2844 helix: -0.28 (0.17), residues: 688 sheet: 1.09 (0.19), residues: 622 loop : -0.72 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.145 0.016 ARG B 567 TYR 0.028 0.005 TYR A 873 PHE 0.037 0.003 PHE B 58 TRP 0.029 0.003 TRP C 886 HIS 0.011 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00866 / 0.35 (23382) covalent geometry : angle 1.03643 / 0.58 (31883) SS BOND : bond 0.00849 / 0.53 ( 36) SS BOND : angle 3.33551 / 2.24 ( 72) hydrogen bonds : bond 0.13600 / 8.74 ( 953) hydrogen bonds : angle 7.48177 / 5.16 ( 2682) link_BETA1-4 : bond 0.01446 / 0.73 ( 11) link_BETA1-4 : angle 3.83340 / 2.52 ( 33) link_NAG-ASN : bond 0.00741 / 0.40 ( 39) link_NAG-ASN : angle 5.56369 / 3.67 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 328 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7513 (t0) cc_final: 0.7145 (t0) REVERT: A 779 GLN cc_start: 0.7859 (tp40) cc_final: 0.7614 (tp40) REVERT: A 974 SER cc_start: 0.8813 (t) cc_final: 0.8568 (t) REVERT: B 28 TYR cc_start: 0.8092 (m-80) cc_final: 0.7648 (m-10) REVERT: B 117 LEU cc_start: 0.7063 (mp) cc_final: 0.6614 (tt) REVERT: B 287 ASP cc_start: 0.7535 (m-30) cc_final: 0.7277 (m-30) REVERT: B 725 GLU cc_start: 0.6674 (tt0) cc_final: 0.6437 (tt0) REVERT: B 768 THR cc_start: 0.7664 (m) cc_final: 0.7382 (t) REVERT: B 779 GLN cc_start: 0.7862 (tt0) cc_final: 0.7484 (mt0) REVERT: B 780 GLU cc_start: 0.8024 (tt0) cc_final: 0.7783 (tt0) REVERT: B 938 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6439 (pp) REVERT: C 43 PHE cc_start: 0.7341 (t80) cc_final: 0.7129 (t80) REVERT: C 310 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8077 (ttpp) REVERT: C 380 TYR cc_start: 0.7397 (m-80) cc_final: 0.7043 (m-80) REVERT: C 776 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7447 (ttpt) REVERT: C 780 GLU cc_start: 0.7434 (tt0) cc_final: 0.7232 (tt0) REVERT: C 935 GLN cc_start: 0.8078 (pt0) cc_final: 0.7809 (tt0) REVERT: C 1127 ASP cc_start: 0.7338 (p0) cc_final: 0.7131 (p0) outliers start: 87 outliers final: 61 residues processed: 402 average time/residue: 0.1473 time to fit residues: 94.4408 Evaluate side-chains 305 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 360 ASN A 370 ASN A 532 ASN A 563 GLN A 580 GLN A 703 ASN A 751 ASN A 913 GLN A 914 ASN A 969 ASN A1101 HIS B 52 GLN B 137 ASN B 207 HIS B 239 GLN B 354 ASN B 409 GLN B 580 GLN B 935 GLN B1005 GLN B1101 HIS B1106 GLN C 134 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 422 ASN C 439 ASN C 755 GLN C 856 ASN C 935 GLN C 969 ASN C1005 GLN C1101 HIS C1106 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.169610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125230 restraints weight = 31273.741| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.47 r_work: 0.3369 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23468 Z= 0.138 Angle : 0.715 19.671 32105 Z= 0.355 Chirality : 0.050 0.703 3857 Planarity : 0.005 0.065 4055 Dihedral : 5.600 55.929 3151 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.68 % Rotamer: Outliers : 3.12 % Allowed : 13.43 % Favored : 83.45 % 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: 0.38 (0.15), residues: 2844 helix: 1.04 (0.20), residues: 686 sheet: 1.17 (0.19), residues: 637 loop : -0.50 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.022 0.001 TYR B 904 PHE 0.015 0.001 PHE A 888 TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (23382) covalent geometry : angle 0.65952 / 0.34 (31883) SS BOND : bond 0.00464 / 0.33 ( 36) SS BOND : angle 2.28367 / 1.37 ( 72) hydrogen bonds : bond 0.05327 / 3.48 ( 953) hydrogen bonds : angle 6.14967 / 4.25 ( 2682) link_BETA1-4 : bond 0.01169 / 0.60 ( 11) link_BETA1-4 : angle 3.07786 / 2.04 ( 33) link_NAG-ASN : bond 0.00548 / 0.29 ( 39) link_NAG-ASN : angle 3.98062 / 2.65 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 261 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5404 (pm20) REVERT: A 273 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6898 (mtt90) REVERT: A 318 PHE cc_start: 0.6686 (t80) cc_final: 0.6288 (t80) REVERT: A 578 ASP cc_start: 0.7356 (t0) cc_final: 0.6939 (p0) REVERT: A 779 GLN cc_start: 0.7999 (tp40) cc_final: 0.7722 (tp40) REVERT: A 1041 ASP cc_start: 0.8209 (m-30) cc_final: 0.7902 (t0) REVERT: B 28 TYR cc_start: 0.8014 (m-80) cc_final: 0.7444 (m-10) REVERT: B 30 ASN cc_start: 0.8343 (p0) cc_final: 0.8133 (p0) REVERT: B 34 ARG cc_start: 0.7442 (mtp85) cc_final: 0.6929 (mtp85) REVERT: B 191 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 237 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6960 (ptm160) REVERT: B 287 ASP cc_start: 0.7854 (m-30) cc_final: 0.7437 (m-30) REVERT: B 618 THR cc_start: 0.8615 (m) cc_final: 0.8398 (p) REVERT: B 742 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7436 (pt) REVERT: B 779 GLN cc_start: 0.8039 (tt0) cc_final: 0.7766 (tt0) REVERT: B 780 GLU cc_start: 0.8462 (tt0) cc_final: 0.8193 (tt0) REVERT: B 1127 ASP cc_start: 0.8480 (m-30) cc_final: 0.8076 (t0) REVERT: B 1132 ILE cc_start: 0.8692 (tt) cc_final: 0.8426 (tt) REVERT: C 306 PHE cc_start: 0.7397 (m-80) cc_final: 0.7026 (m-80) REVERT: C 380 TYR cc_start: 0.7583 (m-80) cc_final: 0.7270 (m-80) REVERT: C 515 PHE cc_start: 0.8468 (m-80) cc_final: 0.8174 (m-80) REVERT: C 535 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7361 (mttp) REVERT: C 776 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7553 (ttpt) REVERT: C 904 TYR cc_start: 0.7145 (t80) cc_final: 0.6907 (t80) REVERT: C 935 GLN cc_start: 0.7950 (pt0) cc_final: 0.7717 (tt0) REVERT: C 1127 ASP cc_start: 0.7676 (p0) cc_final: 0.7472 (p0) outliers start: 75 outliers final: 42 residues processed: 322 average time/residue: 0.1370 time to fit residues: 72.4098 Evaluate side-chains 266 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 198 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 82 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 360 ASN A 856 ASN B 207 HIS B 239 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.166681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119383 restraints weight = 31516.775| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.55 r_work: 0.3319 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23468 Z= 0.151 Angle : 0.664 14.815 32105 Z= 0.329 Chirality : 0.048 0.366 3857 Planarity : 0.004 0.049 4055 Dihedral : 5.056 54.497 3101 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 3.33 % Allowed : 14.35 % Favored : 82.33 % 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: 0.49 (0.15), residues: 2844 helix: 1.32 (0.20), residues: 680 sheet: 1.21 (0.19), residues: 641 loop : -0.52 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE C 541 TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (23382) covalent geometry : angle 0.62116 / 0.32 (31883) SS BOND : bond 0.00730 / 0.44 ( 36) SS BOND : angle 2.20737 / 1.39 ( 72) hydrogen bonds : bond 0.05119 / 3.34 ( 953) hydrogen bonds : angle 5.81227 / 4.01 ( 2682) link_BETA1-4 : bond 0.01142 / 0.58 ( 11) link_BETA1-4 : angle 3.11448 / 2.06 ( 33) link_NAG-ASN : bond 0.00452 / 0.23 ( 39) link_NAG-ASN : angle 3.15913 / 2.14 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 231 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8251 (t) cc_final: 0.7983 (t) REVERT: A 132 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5435 (pm20) REVERT: A 273 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7293 (mtt90) REVERT: A 318 PHE cc_start: 0.6852 (t80) cc_final: 0.6550 (t80) REVERT: A 779 GLN cc_start: 0.8209 (tp40) cc_final: 0.7900 (tp40) REVERT: A 781 VAL cc_start: 0.8080 (t) cc_final: 0.7684 (p) REVERT: A 1041 ASP cc_start: 0.8268 (m-30) cc_final: 0.7966 (t0) REVERT: B 28 TYR cc_start: 0.8096 (m-80) cc_final: 0.7657 (m-10) REVERT: B 30 ASN cc_start: 0.8455 (p0) cc_final: 0.8106 (p0) REVERT: B 34 ARG cc_start: 0.7609 (mtp85) cc_final: 0.6989 (mtp85) REVERT: B 53 ASP cc_start: 0.7492 (t70) cc_final: 0.7240 (t70) REVERT: B 237 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7143 (ptm160) REVERT: B 287 ASP cc_start: 0.7982 (m-30) cc_final: 0.7603 (m-30) REVERT: B 742 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7702 (pt) REVERT: B 779 GLN cc_start: 0.8306 (tt0) cc_final: 0.8035 (tt0) REVERT: B 780 GLU cc_start: 0.8575 (tt0) cc_final: 0.8330 (tt0) REVERT: B 868 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 1127 ASP cc_start: 0.8472 (m-30) cc_final: 0.8227 (t0) REVERT: B 1132 ILE cc_start: 0.8740 (tt) cc_final: 0.8516 (tt) REVERT: C 226 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3681 (tt) REVERT: C 306 PHE cc_start: 0.7441 (m-80) cc_final: 0.7078 (m-80) REVERT: C 535 LYS cc_start: 0.7837 (mmtm) cc_final: 0.7547 (mttp) REVERT: C 584 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5488 (mm) REVERT: C 776 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7781 (tttm) REVERT: C 935 GLN cc_start: 0.8151 (pt0) cc_final: 0.7621 (tt0) outliers start: 80 outliers final: 58 residues processed: 294 average time/residue: 0.1337 time to fit residues: 64.2141 Evaluate side-chains 277 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 192 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 251 optimal weight: 0.6980 chunk 161 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 258 optimal weight: 0.0000 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 703 ASN B 207 HIS B 239 GLN B 544 ASN B 787 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119130 restraints weight = 31351.803| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.55 r_work: 0.3316 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23468 Z= 0.142 Angle : 0.619 14.539 32105 Z= 0.307 Chirality : 0.047 0.360 3857 Planarity : 0.004 0.048 4055 Dihedral : 4.796 52.847 3095 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.28 % Allowed : 14.68 % Favored : 81.04 % 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: 0.49 (0.15), residues: 2844 helix: 1.43 (0.20), residues: 679 sheet: 1.14 (0.19), residues: 653 loop : -0.55 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.001 PHE C 823 TRP 0.009 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (23382) covalent geometry : angle 0.58241 / 0.30 (31883) SS BOND : bond 0.00497 / 0.32 ( 36) SS BOND : angle 2.16394 / 1.40 ( 72) hydrogen bonds : bond 0.04787 / 3.12 ( 953) hydrogen bonds : angle 5.50421 / 3.79 ( 2682) link_BETA1-4 : bond 0.01048 / 0.54 ( 11) link_BETA1-4 : angle 2.97426 / 1.98 ( 33) link_NAG-ASN : bond 0.00376 / 0.19 ( 39) link_NAG-ASN : angle 2.70424 / 1.82 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 229 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8364 (t) cc_final: 0.8085 (t) REVERT: A 132 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5273 (pm20) REVERT: A 273 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7316 (mtt90) REVERT: A 318 PHE cc_start: 0.6847 (t80) cc_final: 0.6572 (t80) REVERT: A 556 ASN cc_start: 0.8501 (p0) cc_final: 0.8193 (m-40) REVERT: A 578 ASP cc_start: 0.7447 (t0) cc_final: 0.7036 (p0) REVERT: A 703 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8205 (p0) REVERT: A 779 GLN cc_start: 0.8248 (tp40) cc_final: 0.7942 (tp40) REVERT: A 781 VAL cc_start: 0.8065 (t) cc_final: 0.7663 (p) REVERT: A 1029 MET cc_start: 0.8194 (tpp) cc_final: 0.7867 (ttm) REVERT: B 28 TYR cc_start: 0.8103 (m-80) cc_final: 0.7711 (m-10) REVERT: B 30 ASN cc_start: 0.8415 (p0) cc_final: 0.8150 (p0) REVERT: B 237 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7171 (ptp-110) REVERT: B 779 GLN cc_start: 0.8295 (tt0) cc_final: 0.8050 (tt0) REVERT: B 780 GLU cc_start: 0.8583 (tt0) cc_final: 0.8359 (tt0) REVERT: B 868 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8086 (tt0) REVERT: B 1037 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 1127 ASP cc_start: 0.8536 (m-30) cc_final: 0.8299 (t0) REVERT: B 1132 ILE cc_start: 0.8758 (tt) cc_final: 0.8536 (tt) REVERT: B 1137 VAL cc_start: 0.8527 (t) cc_final: 0.8234 (m) REVERT: C 204 TYR cc_start: 0.5651 (m-80) cc_final: 0.5374 (m-80) REVERT: C 226 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3829 (tt) REVERT: C 306 PHE cc_start: 0.7371 (m-80) cc_final: 0.6992 (m-80) REVERT: C 584 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.5257 (mm) REVERT: C 776 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7826 (tttm) REVERT: C 788 ILE cc_start: 0.8365 (mm) cc_final: 0.8116 (mt) outliers start: 103 outliers final: 69 residues processed: 312 average time/residue: 0.1327 time to fit residues: 68.8848 Evaluate side-chains 294 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 184 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 856 ASN A 949 GLN B 207 HIS B 239 GLN B 394 ASN B 655 HIS ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116787 restraints weight = 31248.419| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.53 r_work: 0.3285 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23468 Z= 0.203 Angle : 0.648 13.965 32105 Z= 0.323 Chirality : 0.049 0.345 3857 Planarity : 0.005 0.048 4055 Dihedral : 4.898 51.635 3094 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.70 % Allowed : 15.26 % Favored : 80.04 % 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 (0.15), residues: 2844 helix: 1.28 (0.20), residues: 680 sheet: 1.00 (0.19), residues: 665 loop : -0.66 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1107 TYR 0.018 0.002 TYR B1067 PHE 0.023 0.002 PHE C 823 TRP 0.009 0.001 TRP C 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.20 (23382) covalent geometry : angle 0.61258 / 0.31 (31883) SS BOND : bond 0.00627 / 0.39 ( 36) SS BOND : angle 2.42317 / 1.58 ( 72) hydrogen bonds : bond 0.05414 / 3.54 ( 953) hydrogen bonds : angle 5.52046 / 3.80 ( 2682) link_BETA1-4 : bond 0.00966 / 0.49 ( 11) link_BETA1-4 : angle 2.90498 / 1.95 ( 33) link_NAG-ASN : bond 0.00417 / 0.22 ( 39) link_NAG-ASN : angle 2.67276 / 1.80 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 229 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8448 (t) cc_final: 0.8174 (t) REVERT: A 132 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5359 (pm20) REVERT: A 273 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7312 (mtt90) REVERT: A 318 PHE cc_start: 0.6891 (t80) cc_final: 0.6606 (t80) REVERT: A 556 ASN cc_start: 0.8546 (p0) cc_final: 0.8207 (m-40) REVERT: A 578 ASP cc_start: 0.7463 (t0) cc_final: 0.6920 (p0) REVERT: A 748 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: A 779 GLN cc_start: 0.8259 (tp40) cc_final: 0.7965 (tp40) REVERT: A 781 VAL cc_start: 0.8144 (t) cc_final: 0.7756 (p) REVERT: B 28 TYR cc_start: 0.8149 (m-80) cc_final: 0.7614 (m-10) REVERT: B 30 ASN cc_start: 0.8362 (p0) cc_final: 0.8100 (p0) REVERT: B 237 ARG cc_start: 0.7517 (mtm180) cc_final: 0.7180 (ptp-110) REVERT: B 779 GLN cc_start: 0.8316 (tt0) cc_final: 0.8033 (tt0) REVERT: B 780 GLU cc_start: 0.8576 (tt0) cc_final: 0.8317 (tt0) REVERT: B 868 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8196 (tt0) REVERT: B 1037 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8260 (p) REVERT: B 1127 ASP cc_start: 0.8534 (m-30) cc_final: 0.8249 (t0) REVERT: B 1132 ILE cc_start: 0.8750 (tt) cc_final: 0.8515 (tt) REVERT: B 1137 VAL cc_start: 0.8614 (t) cc_final: 0.8365 (m) REVERT: C 226 LEU cc_start: 0.4123 (OUTLIER) cc_final: 0.3790 (tt) REVERT: C 306 PHE cc_start: 0.7348 (m-80) cc_final: 0.6952 (m-80) REVERT: C 495 TYR cc_start: 0.4314 (OUTLIER) cc_final: 0.1187 (t80) REVERT: C 563 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: C 650 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7682 (tt) REVERT: C 776 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7788 (tttm) REVERT: C 788 ILE cc_start: 0.8397 (mm) cc_final: 0.8157 (mt) REVERT: C 1130 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8286 (mt) outliers start: 113 outliers final: 75 residues processed: 318 average time/residue: 0.1348 time to fit residues: 71.7630 Evaluate side-chains 307 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 271 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 236 optimal weight: 0.6980 chunk 283 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 360 ASN A 703 ASN A 856 ASN A 949 GLN B 207 HIS B 239 GLN C 280 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117342 restraints weight = 31336.271| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.55 r_work: 0.3294 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 23468 Z= 0.163 Angle : 0.630 14.330 32105 Z= 0.313 Chirality : 0.047 0.348 3857 Planarity : 0.004 0.047 4055 Dihedral : 4.676 50.410 3091 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.20 % Allowed : 16.38 % Favored : 79.42 % 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: 0.30 (0.15), residues: 2844 helix: 1.30 (0.20), residues: 682 sheet: 1.04 (0.19), residues: 660 loop : -0.71 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE C 823 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (23382) covalent geometry : angle 0.59127 / 0.30 (31883) SS BOND : bond 0.00611 / 0.38 ( 36) SS BOND : angle 2.78369 / 1.70 ( 72) hydrogen bonds : bond 0.05030 / 3.27 ( 953) hydrogen bonds : angle 5.47648 / 3.78 ( 2682) link_BETA1-4 : bond 0.01078 / 0.55 ( 11) link_BETA1-4 : angle 2.85284 / 1.91 ( 33) link_NAG-ASN : bond 0.00367 / 0.19 ( 39) link_NAG-ASN : angle 2.56350 / 1.73 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 229 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8458 (t) cc_final: 0.8189 (t) REVERT: A 132 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5320 (pm20) REVERT: A 556 ASN cc_start: 0.8553 (p0) cc_final: 0.8220 (m-40) REVERT: A 748 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: A 779 GLN cc_start: 0.8250 (tp40) cc_final: 0.7955 (tp40) REVERT: A 781 VAL cc_start: 0.8110 (t) cc_final: 0.7704 (p) REVERT: B 28 TYR cc_start: 0.8154 (m-80) cc_final: 0.7725 (m-10) REVERT: B 30 ASN cc_start: 0.8347 (p0) cc_final: 0.8094 (p0) REVERT: B 237 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7144 (ptp-110) REVERT: B 779 GLN cc_start: 0.8304 (tt0) cc_final: 0.8003 (tt0) REVERT: B 780 GLU cc_start: 0.8566 (tt0) cc_final: 0.8310 (tt0) REVERT: B 868 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8127 (tt0) REVERT: B 1037 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8251 (p) REVERT: B 1127 ASP cc_start: 0.8501 (m-30) cc_final: 0.8211 (t0) REVERT: B 1132 ILE cc_start: 0.8736 (tt) cc_final: 0.8495 (tt) REVERT: B 1137 VAL cc_start: 0.8660 (t) cc_final: 0.8411 (m) REVERT: C 204 TYR cc_start: 0.5627 (m-80) cc_final: 0.5321 (m-80) REVERT: C 226 LEU cc_start: 0.4145 (OUTLIER) cc_final: 0.3792 (tt) REVERT: C 306 PHE cc_start: 0.7356 (m-80) cc_final: 0.6975 (m-80) REVERT: C 495 TYR cc_start: 0.4263 (OUTLIER) cc_final: 0.1177 (t80) REVERT: C 563 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: C 650 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7652 (tt) REVERT: C 776 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7790 (tttm) REVERT: C 788 ILE cc_start: 0.8389 (mm) cc_final: 0.8154 (mt) REVERT: C 904 TYR cc_start: 0.7367 (t80) cc_final: 0.7059 (t80) REVERT: C 1130 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8304 (mt) outliers start: 101 outliers final: 77 residues processed: 309 average time/residue: 0.1334 time to fit residues: 69.0950 Evaluate side-chains 312 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 227 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 149 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 273 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 chunk 263 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 224 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 172 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 207 HIS B 239 GLN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117831 restraints weight = 31375.544| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.56 r_work: 0.3302 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23468 Z= 0.151 Angle : 0.610 13.244 32105 Z= 0.302 Chirality : 0.047 0.331 3857 Planarity : 0.004 0.047 4055 Dihedral : 4.564 47.617 3091 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.16 % Allowed : 16.88 % Favored : 78.96 % 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 (0.15), residues: 2844 helix: 1.40 (0.21), residues: 683 sheet: 1.08 (0.19), residues: 647 loop : -0.75 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE C 823 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (23382) covalent geometry : angle 0.57611 / 0.29 (31883) SS BOND : bond 0.00568 / 0.35 ( 36) SS BOND : angle 2.36397 / 1.52 ( 72) hydrogen bonds : bond 0.04802 / 3.11 ( 953) hydrogen bonds : angle 5.37932 / 3.71 ( 2682) link_BETA1-4 : bond 0.00914 / 0.47 ( 11) link_BETA1-4 : angle 2.77804 / 1.87 ( 33) link_NAG-ASN : bond 0.00349 / 0.17 ( 39) link_NAG-ASN : angle 2.42640 / 1.63 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 224 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8478 (t) cc_final: 0.8191 (t) REVERT: A 132 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5252 (pm20) REVERT: A 238 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7065 (p90) REVERT: A 556 ASN cc_start: 0.8536 (p0) cc_final: 0.8161 (m-40) REVERT: A 578 ASP cc_start: 0.7328 (t0) cc_final: 0.6964 (p0) REVERT: A 748 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: A 779 GLN cc_start: 0.8292 (tp40) cc_final: 0.8006 (tp40) REVERT: B 28 TYR cc_start: 0.8148 (m-80) cc_final: 0.7646 (m-10) REVERT: B 30 ASN cc_start: 0.8263 (p0) cc_final: 0.8054 (p0) REVERT: B 191 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7991 (mt-10) REVERT: B 237 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7163 (ptp-110) REVERT: B 779 GLN cc_start: 0.8226 (tt0) cc_final: 0.7940 (tt0) REVERT: B 780 GLU cc_start: 0.8543 (tt0) cc_final: 0.8304 (tt0) REVERT: B 868 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8138 (tt0) REVERT: B 1132 ILE cc_start: 0.8710 (tt) cc_final: 0.8468 (tt) REVERT: B 1137 VAL cc_start: 0.8666 (t) cc_final: 0.8419 (m) REVERT: C 204 TYR cc_start: 0.5581 (m-80) cc_final: 0.5254 (m-80) REVERT: C 226 LEU cc_start: 0.4106 (OUTLIER) cc_final: 0.3766 (tt) REVERT: C 306 PHE cc_start: 0.7470 (m-80) cc_final: 0.7132 (m-80) REVERT: C 495 TYR cc_start: 0.4283 (OUTLIER) cc_final: 0.1163 (t80) REVERT: C 584 ILE cc_start: 0.5673 (OUTLIER) cc_final: 0.5351 (mm) REVERT: C 650 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7576 (tt) REVERT: C 776 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7766 (tttm) REVERT: C 788 ILE cc_start: 0.8358 (mm) cc_final: 0.8134 (mt) REVERT: C 1130 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8329 (mt) outliers start: 100 outliers final: 74 residues processed: 301 average time/residue: 0.1317 time to fit residues: 66.5158 Evaluate side-chains 300 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 218 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 16 optimal weight: 1.9990 chunk 275 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 288 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN A 856 ASN A 913 GLN B 207 HIS B 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117521 restraints weight = 31126.724| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.52 r_work: 0.3265 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23468 Z= 0.191 Angle : 0.639 13.186 32105 Z= 0.317 Chirality : 0.048 0.315 3857 Planarity : 0.004 0.047 4055 Dihedral : 4.620 48.322 3088 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.20 % Allowed : 17.38 % Favored : 78.42 % 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 (0.15), residues: 2844 helix: 1.30 (0.21), residues: 683 sheet: 0.86 (0.19), residues: 673 loop : -0.79 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.018 0.001 TYR B1067 PHE 0.029 0.002 PHE C 823 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (23382) covalent geometry : angle 0.60640 / 0.31 (31883) SS BOND : bond 0.00629 / 0.38 ( 36) SS BOND : angle 2.39925 / 1.60 ( 72) hydrogen bonds : bond 0.05279 / 3.43 ( 953) hydrogen bonds : angle 5.40335 / 3.72 ( 2682) link_BETA1-4 : bond 0.00846 / 0.44 ( 11) link_BETA1-4 : angle 2.74822 / 1.86 ( 33) link_NAG-ASN : bond 0.00388 / 0.20 ( 39) link_NAG-ASN : angle 2.45879 / 1.66 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 221 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8532 (t) cc_final: 0.8267 (t) REVERT: A 120 VAL cc_start: 0.7559 (t) cc_final: 0.7349 (t) REVERT: A 132 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5355 (pm20) REVERT: A 556 ASN cc_start: 0.8549 (p0) cc_final: 0.8221 (m-40) REVERT: A 578 ASP cc_start: 0.7427 (t0) cc_final: 0.7039 (p0) REVERT: A 748 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: A 779 GLN cc_start: 0.8355 (tp40) cc_final: 0.8061 (tp40) REVERT: A 781 VAL cc_start: 0.8173 (t) cc_final: 0.7788 (p) REVERT: B 191 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 237 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7207 (ptp-110) REVERT: B 780 GLU cc_start: 0.8575 (tt0) cc_final: 0.8311 (tt0) REVERT: B 868 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 1132 ILE cc_start: 0.8749 (tt) cc_final: 0.8485 (tt) REVERT: B 1137 VAL cc_start: 0.8696 (t) cc_final: 0.8448 (m) REVERT: C 108 THR cc_start: 0.3194 (OUTLIER) cc_final: 0.2923 (p) REVERT: C 226 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3903 (tt) REVERT: C 306 PHE cc_start: 0.7367 (m-80) cc_final: 0.6981 (m-80) REVERT: C 495 TYR cc_start: 0.4363 (OUTLIER) cc_final: 0.1244 (t80) REVERT: C 584 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5530 (mm) REVERT: C 650 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7626 (tt) REVERT: C 776 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7829 (tttm) REVERT: C 788 ILE cc_start: 0.8441 (mm) cc_final: 0.8213 (mt) REVERT: C 904 TYR cc_start: 0.7367 (t80) cc_final: 0.7072 (t80) REVERT: C 1130 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8484 (mt) outliers start: 101 outliers final: 82 residues processed: 300 average time/residue: 0.1305 time to fit residues: 65.7074 Evaluate side-chains 307 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 33 optimal weight: 8.9990 chunk 274 optimal weight: 0.0020 chunk 238 optimal weight: 0.8980 chunk 275 optimal weight: 0.9980 chunk 236 optimal weight: 0.0370 chunk 136 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 203 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 94 optimal weight: 0.5980 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 207 HIS B 239 GLN B 901 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.166383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119745 restraints weight = 31331.077| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.55 r_work: 0.3314 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23468 Z= 0.114 Angle : 0.584 12.863 32105 Z= 0.288 Chirality : 0.046 0.313 3857 Planarity : 0.004 0.046 4055 Dihedral : 4.350 46.470 3088 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.41 % Allowed : 18.34 % Favored : 78.25 % 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: 0.35 (0.15), residues: 2844 helix: 1.49 (0.21), residues: 684 sheet: 1.03 (0.19), residues: 660 loop : -0.75 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.018 0.001 TYR B1067 PHE 0.028 0.001 PHE C 823 TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (23382) covalent geometry : angle 0.55487 / 0.28 (31883) SS BOND : bond 0.00521 / 0.32 ( 36) SS BOND : angle 1.93627 / 1.31 ( 72) hydrogen bonds : bond 0.04304 / 2.79 ( 953) hydrogen bonds : angle 5.23529 / 3.62 ( 2682) link_BETA1-4 : bond 0.00896 / 0.47 ( 11) link_BETA1-4 : angle 2.70262 / 1.83 ( 33) link_NAG-ASN : bond 0.00323 / 0.16 ( 39) link_NAG-ASN : angle 2.27638 / 1.52 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8466 (t) cc_final: 0.8213 (t) REVERT: A 120 VAL cc_start: 0.7557 (t) cc_final: 0.7339 (t) REVERT: A 132 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5256 (pm20) REVERT: A 532 ASN cc_start: 0.8029 (m-40) cc_final: 0.7268 (t0) REVERT: A 556 ASN cc_start: 0.8528 (p0) cc_final: 0.8130 (m110) REVERT: A 578 ASP cc_start: 0.7437 (t0) cc_final: 0.6999 (p0) REVERT: A 641 ASN cc_start: 0.6507 (t0) cc_final: 0.6106 (m110) REVERT: A 748 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: A 779 GLN cc_start: 0.8311 (tp40) cc_final: 0.8001 (tp40) REVERT: B 191 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 237 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7172 (ptp-110) REVERT: B 780 GLU cc_start: 0.8538 (tt0) cc_final: 0.8329 (tt0) REVERT: B 868 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 1132 ILE cc_start: 0.8716 (tt) cc_final: 0.8465 (tt) REVERT: B 1137 VAL cc_start: 0.8661 (t) cc_final: 0.8388 (m) REVERT: C 204 TYR cc_start: 0.5518 (m-80) cc_final: 0.5210 (m-80) REVERT: C 226 LEU cc_start: 0.4060 (OUTLIER) cc_final: 0.3712 (tt) REVERT: C 306 PHE cc_start: 0.7461 (m-80) cc_final: 0.7121 (m-80) REVERT: C 429 PHE cc_start: 0.8452 (t80) cc_final: 0.7781 (t80) REVERT: C 584 ILE cc_start: 0.5818 (OUTLIER) cc_final: 0.5579 (mm) REVERT: C 650 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7574 (tt) REVERT: C 776 LYS cc_start: 0.8385 (ttmm) cc_final: 0.7760 (tttm) REVERT: C 788 ILE cc_start: 0.8394 (mm) cc_final: 0.8164 (mt) REVERT: C 1130 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8389 (mt) outliers start: 82 outliers final: 62 residues processed: 297 average time/residue: 0.1334 time to fit residues: 66.3424 Evaluate side-chains 294 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 182 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 169 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 207 HIS B 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.165565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118974 restraints weight = 31161.792| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.52 r_work: 0.3286 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23468 Z= 0.145 Angle : 0.603 12.774 32105 Z= 0.298 Chirality : 0.047 0.306 3857 Planarity : 0.004 0.046 4055 Dihedral : 4.357 46.218 3087 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.04 % Allowed : 18.92 % Favored : 78.05 % 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: 0.31 (0.15), residues: 2844 helix: 1.48 (0.21), residues: 683 sheet: 0.96 (0.19), residues: 667 loop : -0.77 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.018 0.001 TYR B1067 PHE 0.027 0.001 PHE C 823 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 (23382) covalent geometry : angle 0.57481 / 0.29 (31883) SS BOND : bond 0.00570 / 0.35 ( 36) SS BOND : angle 2.02526 / 1.38 ( 72) hydrogen bonds : bond 0.04669 / 3.03 ( 953) hydrogen bonds : angle 5.22995 / 3.61 ( 2682) link_BETA1-4 : bond 0.00816 / 0.42 ( 11) link_BETA1-4 : angle 2.67897 / 1.82 ( 33) link_NAG-ASN : bond 0.00340 / 0.17 ( 39) link_NAG-ASN : angle 2.29025 / 1.54 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 226 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8500 (t) cc_final: 0.8250 (t) REVERT: A 120 VAL cc_start: 0.7536 (t) cc_final: 0.7320 (t) REVERT: A 132 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5315 (pm20) REVERT: A 532 ASN cc_start: 0.8030 (m-40) cc_final: 0.7292 (t0) REVERT: A 556 ASN cc_start: 0.8505 (p0) cc_final: 0.8092 (m110) REVERT: A 641 ASN cc_start: 0.6539 (t0) cc_final: 0.6159 (m110) REVERT: A 748 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: A 779 GLN cc_start: 0.8322 (tp40) cc_final: 0.8019 (tp40) REVERT: B 191 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 237 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7222 (ptp-110) REVERT: B 780 GLU cc_start: 0.8555 (tt0) cc_final: 0.8340 (tt0) REVERT: B 868 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 1037 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 1132 ILE cc_start: 0.8743 (tt) cc_final: 0.8490 (tt) REVERT: B 1137 VAL cc_start: 0.8678 (t) cc_final: 0.8433 (m) REVERT: C 204 TYR cc_start: 0.5557 (m-80) cc_final: 0.5238 (m-80) REVERT: C 226 LEU cc_start: 0.4138 (OUTLIER) cc_final: 0.3767 (tt) REVERT: C 306 PHE cc_start: 0.7474 (m-80) cc_final: 0.7133 (m-80) REVERT: C 429 PHE cc_start: 0.8494 (t80) cc_final: 0.7820 (t80) REVERT: C 584 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5586 (mm) REVERT: C 650 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7634 (tt) REVERT: C 776 LYS cc_start: 0.8390 (ttmm) cc_final: 0.7796 (tttm) REVERT: C 788 ILE cc_start: 0.8407 (mm) cc_final: 0.8181 (mt) REVERT: C 1130 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8344 (mt) outliers start: 73 outliers final: 65 residues processed: 285 average time/residue: 0.1372 time to fit residues: 65.0240 Evaluate side-chains 297 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 225 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 204 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 277 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 207 HIS B 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117705 restraints weight = 31132.975| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.52 r_work: 0.3283 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23468 Z= 0.176 Angle : 0.621 12.518 32105 Z= 0.308 Chirality : 0.048 0.301 3857 Planarity : 0.004 0.046 4055 Dihedral : 4.459 46.250 3087 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.37 % Allowed : 18.54 % Favored : 78.09 % 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: 0.23 (0.15), residues: 2844 helix: 1.40 (0.21), residues: 683 sheet: 0.87 (0.19), residues: 672 loop : -0.80 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.018 0.001 TYR B1067 PHE 0.027 0.002 PHE C 823 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (23382) covalent geometry : angle 0.59219 / 0.30 (31883) SS BOND : bond 0.00591 / 0.36 ( 36) SS BOND : angle 2.08070 / 1.40 ( 72) hydrogen bonds : bond 0.05015 / 3.25 ( 953) hydrogen bonds : angle 5.28760 / 3.65 ( 2682) link_BETA1-4 : bond 0.00791 / 0.41 ( 11) link_BETA1-4 : angle 2.67201 / 1.83 ( 33) link_NAG-ASN : bond 0.00353 / 0.18 ( 39) link_NAG-ASN : angle 2.33777 / 1.57 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7009.86 seconds wall clock time: 120 minutes 22.24 seconds (7222.24 seconds total)