Starting phenix.real_space_refine on Thu Mar 5 23:48:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xiy_33212/03_2026/7xiy_33212.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xiy_33212/03_2026/7xiy_33212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xiy_33212/03_2026/7xiy_33212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xiy_33212/03_2026/7xiy_33212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xiy_33212/03_2026/7xiy_33212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xiy_33212/03_2026/7xiy_33212.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16645 2.51 5 N 4277 2.21 5 O 5056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26089 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 8477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8477 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 8477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8477 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8477 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.29, per 1000 atoms: 0.24 Number of scatterers: 26089 At special positions: 0 Unit cell: (148.72, 143.52, 177.84, 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 111 16.00 O 5056 8.00 N 4277 7.00 C 16645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 343 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B1134 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 47 sheets defined 21.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.842A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.533A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.973A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.684A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.220A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.310A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.785A 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 removed outlier: 3.729A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 982' Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.074A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 3.946A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 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 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 850 through 856 removed outlier: 3.834A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.524A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.266A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.904A 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 982 removed outlier: 3.916A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.114A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1149 removed outlier: 3.654A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.589A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.657A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.563A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.052A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 850 through 856 removed outlier: 3.583A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.393A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.400A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.789A 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 977 through 982 removed outlier: 4.034A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 977 through 982' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.932A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1149 removed outlier: 3.982A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.774A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 131 removed outlier: 3.509A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.994A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.741A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.358A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 538 through 539 removed outlier: 4.826A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.269A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.857A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.791A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.502A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.515A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.558A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AC3, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.341A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AC6, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.870A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.381A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.232A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 659 through 660 removed outlier: 4.424A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.878A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.395A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.395A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.614A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.109A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 126 through 131 removed outlier: 3.533A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 276 through 279 removed outlier: 3.975A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.811A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.132A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.132A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 659 through 660 removed outlier: 4.204A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.829A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.602A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 833 hydrogen bonds defined for protein. 2313 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: 5.92 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 1 1.14 - 1.31: 4219 1.31 - 1.49: 11413 1.49 - 1.67: 10939 1.67 - 1.85: 138 Bond restraints: 26710 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 0.959 0.544 3.40e-02 8.65e+02 2.56e+02 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" CG PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 1.503 1.263 0.240 3.40e-02 8.65e+02 5.00e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 26705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 36223 4.93 - 9.85: 143 9.85 - 14.78: 7 14.78 - 19.70: 6 19.70 - 24.63: 1 Bond angle restraints: 36380 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 78.57 24.63 1.50e+00 4.44e-01 2.70e+02 angle pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 112.00 94.90 17.10 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 95.40 16.60 1.40e+00 5.10e-01 1.41e+02 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 95.75 16.25 1.40e+00 5.10e-01 1.35e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 96.27 15.73 1.40e+00 5.10e-01 1.26e+02 ... (remaining 36375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 14530 21.85 - 43.69: 1566 43.69 - 65.54: 264 65.54 - 87.39: 63 87.39 - 109.24: 68 Dihedral angle restraints: 16491 sinusoidal: 7008 harmonic: 9483 Sorted by residual: dihedral pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " pdb=" CA PRO C 621 " ideal model delta harmonic sigma weight residual -180.00 -128.61 -51.39 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta harmonic sigma weight residual -180.00 -130.61 -49.39 0 5.00e+00 4.00e-02 9.76e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 4.84 88.16 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 16488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3701 0.082 - 0.163: 511 0.163 - 0.245: 22 0.245 - 0.327: 7 0.327 - 0.408: 5 Chirality restraints: 4246 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" C PRO B 217 " pdb=" CB PRO B 217 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 4243 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.127 5.00e-02 4.00e+02 1.76e-01 4.96e+01 pdb=" N PRO C 373 " 0.304 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.095 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " 0.120 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 217 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.115 5.00e-02 4.00e+02 1.60e-01 4.09e+01 pdb=" N PRO A 384 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.079 5.00e-02 4.00e+02 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6348 2.79 - 3.32: 22774 3.32 - 3.85: 43336 3.85 - 4.37: 47426 4.37 - 4.90: 83683 Nonbonded interactions: 203567 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 383 " pdb=" OD1 ASP A 985 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD2 ASP C 994 " model vdw 2.281 3.040 nonbonded pdb=" O ILE C 332 " pdb=" NZ LYS C 528 " model vdw 2.284 3.120 nonbonded pdb=" O LEU C 296 " pdb=" OG1 THR C 299 " model vdw 2.285 3.040 ... (remaining 203562 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' selection = (chain 'B' and resid 29 through 1307) selection = (chain 'C' and resid 29 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' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.280 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.544 26790 Z= 0.243 Angle : 0.871 24.629 36587 Z= 0.458 Chirality : 0.054 0.408 4246 Planarity : 0.008 0.176 4655 Dihedral : 19.041 109.237 10296 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.63 % Favored : 92.03 % Rotamer: Outliers : 0.18 % Allowed : 28.57 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3237 helix: 0.09 (0.19), residues: 648 sheet: -1.03 (0.20), residues: 666 loop : -2.49 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.030 0.001 TYR B 904 PHE 0.040 0.002 PHE A 338 TRP 0.038 0.002 TRP A 633 HIS 0.009 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00589 (26710) covalent geometry : angle 0.85715 (36380) SS BOND : bond 0.00335 ( 33) SS BOND : angle 1.36839 ( 66) hydrogen bonds : bond 0.21295 ( 803) hydrogen bonds : angle 8.20493 ( 2313) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.28862 ( 36) link_NAG-ASN : bond 0.00795 ( 35) link_NAG-ASN : angle 2.84408 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 411 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 619 GLU cc_start: 0.5812 (mt-10) cc_final: 0.5577 (mp0) REVERT: B 751 ASN cc_start: 0.8384 (m-40) cc_final: 0.8175 (m-40) REVERT: B 869 MET cc_start: 0.8400 (mtm) cc_final: 0.8157 (mtm) REVERT: B 950 ASP cc_start: 0.7251 (m-30) cc_final: 0.6893 (m-30) REVERT: A 645 THR cc_start: 0.8714 (m) cc_final: 0.8490 (p) REVERT: A 697 MET cc_start: 0.7640 (mtp) cc_final: 0.7436 (mtp) REVERT: C 269 TYR cc_start: 0.6986 (m-10) cc_final: 0.6699 (m-10) REVERT: C 271 GLN cc_start: 0.8328 (tt0) cc_final: 0.8021 (mt0) REVERT: C 306 PHE cc_start: 0.8154 (m-80) cc_final: 0.7920 (m-10) REVERT: C 388 ASN cc_start: 0.6830 (p0) cc_final: 0.6132 (p0) REVERT: C 525 CYS cc_start: 0.4790 (p) cc_final: 0.4195 (p) REVERT: C 747 THR cc_start: 0.8092 (t) cc_final: 0.7636 (m) REVERT: C 751 ASN cc_start: 0.8134 (m-40) cc_final: 0.7856 (m110) REVERT: C 759 PHE cc_start: 0.7202 (t80) cc_final: 0.6499 (t80) REVERT: C 869 MET cc_start: 0.8042 (ptp) cc_final: 0.7751 (ptp) REVERT: C 950 ASP cc_start: 0.7340 (m-30) cc_final: 0.7134 (m-30) outliers start: 5 outliers final: 2 residues processed: 415 average time/residue: 0.1848 time to fit residues: 120.1125 Evaluate side-chains 195 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 785 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 774 GLN B 955 ASN B1101 HIS A 49 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 751 ASN A 774 GLN A 872 GLN A 955 ASN A 992 GLN A1101 HIS C 49 HIS C 125 ASN C 901 GLN C 955 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.197043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134819 restraints weight = 40337.866| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.95 r_work: 0.3548 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 26790 Z= 0.164 Angle : 0.681 10.027 36587 Z= 0.341 Chirality : 0.049 0.349 4246 Planarity : 0.006 0.142 4655 Dihedral : 11.587 95.062 4482 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.63 % Favored : 92.03 % Rotamer: Outliers : 3.67 % Allowed : 24.90 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3237 helix: 0.74 (0.20), residues: 678 sheet: -0.66 (0.21), residues: 570 loop : -2.48 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 567 TYR 0.025 0.001 TYR A 904 PHE 0.022 0.002 PHE C 338 TRP 0.019 0.002 TRP C 633 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00379 (26710) covalent geometry : angle 0.66177 (36380) SS BOND : bond 0.00414 ( 33) SS BOND : angle 1.58803 ( 66) hydrogen bonds : bond 0.04598 ( 803) hydrogen bonds : angle 5.92601 ( 2313) link_BETA1-4 : bond 0.00176 ( 12) link_BETA1-4 : angle 1.49999 ( 36) link_NAG-ASN : bond 0.00617 ( 35) link_NAG-ASN : angle 2.74337 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 217 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.5019 (t70) cc_final: 0.4794 (t70) REVERT: B 337 PRO cc_start: 0.6493 (Cg_exo) cc_final: 0.5958 (Cg_endo) REVERT: B 374 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.4316 (t80) REVERT: B 663 ASP cc_start: 0.7537 (t0) cc_final: 0.7278 (t0) REVERT: B 751 ASN cc_start: 0.8517 (m-40) cc_final: 0.8199 (m-40) REVERT: B 950 ASP cc_start: 0.8234 (m-30) cc_final: 0.7702 (m-30) REVERT: B 1002 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7869 (tp40) REVERT: A 409 GLN cc_start: 0.5642 (OUTLIER) cc_final: 0.3969 (tt0) REVERT: A 580 GLN cc_start: 0.4677 (OUTLIER) cc_final: 0.4262 (mp10) REVERT: A 645 THR cc_start: 0.8795 (m) cc_final: 0.8498 (p) REVERT: A 697 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8156 (mtp) REVERT: A 773 GLU cc_start: 0.8338 (tp30) cc_final: 0.8110 (tt0) REVERT: A 979 ASP cc_start: 0.7815 (m-30) cc_final: 0.6746 (t0) REVERT: C 104 TRP cc_start: 0.6807 (m-90) cc_final: 0.6425 (m-90) REVERT: C 271 GLN cc_start: 0.8683 (tt0) cc_final: 0.8317 (mt0) REVERT: C 321 GLN cc_start: 0.7525 (mm110) cc_final: 0.7115 (mp10) REVERT: C 335 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6817 (pp) REVERT: C 388 ASN cc_start: 0.7189 (p0) cc_final: 0.6694 (p0) REVERT: C 525 CYS cc_start: 0.5610 (p) cc_final: 0.5288 (t) REVERT: C 537 LYS cc_start: 0.6861 (tmtt) cc_final: 0.6631 (tttp) REVERT: C 565 PHE cc_start: 0.6968 (m-10) cc_final: 0.6762 (m-10) REVERT: C 747 THR cc_start: 0.7877 (t) cc_final: 0.7367 (m) REVERT: C 751 ASN cc_start: 0.8359 (m-40) cc_final: 0.7970 (m-40) REVERT: C 759 PHE cc_start: 0.7826 (t80) cc_final: 0.6819 (t80) REVERT: C 918 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: C 950 ASP cc_start: 0.8125 (m-30) cc_final: 0.7883 (m-30) outliers start: 104 outliers final: 42 residues processed: 304 average time/residue: 0.1560 time to fit residues: 80.2145 Evaluate side-chains 226 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 65 optimal weight: 0.5980 chunk 172 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 chunk 318 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN A 49 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.196344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135151 restraints weight = 40222.505| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.93 r_work: 0.3528 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26790 Z= 0.124 Angle : 0.629 13.149 36587 Z= 0.311 Chirality : 0.047 0.336 4246 Planarity : 0.006 0.138 4655 Dihedral : 10.066 92.388 4479 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.51 % Favored : 92.18 % Rotamer: Outliers : 3.53 % Allowed : 23.88 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.14), residues: 3237 helix: 1.11 (0.21), residues: 678 sheet: -0.42 (0.21), residues: 561 loop : -2.39 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 567 TYR 0.022 0.001 TYR A 904 PHE 0.014 0.001 PHE B 338 TRP 0.018 0.001 TRP B 886 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00282 (26710) covalent geometry : angle 0.61265 (36380) SS BOND : bond 0.00476 ( 33) SS BOND : angle 1.31329 ( 66) hydrogen bonds : bond 0.04207 ( 803) hydrogen bonds : angle 5.57709 ( 2313) link_BETA1-4 : bond 0.00240 ( 12) link_BETA1-4 : angle 1.42349 ( 36) link_NAG-ASN : bond 0.00589 ( 35) link_NAG-ASN : angle 2.49545 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 199 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5512 (mt) REVERT: B 337 PRO cc_start: 0.5840 (Cg_exo) cc_final: 0.5536 (Cg_endo) REVERT: B 374 PHE cc_start: 0.4561 (OUTLIER) cc_final: 0.4211 (t80) REVERT: B 751 ASN cc_start: 0.8448 (m-40) cc_final: 0.8147 (m-40) REVERT: B 912 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8732 (p) REVERT: B 950 ASP cc_start: 0.8237 (m-30) cc_final: 0.7686 (m-30) REVERT: B 964 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8569 (mtmm) REVERT: B 994 ASP cc_start: 0.8745 (t70) cc_final: 0.8482 (t0) REVERT: A 337 PRO cc_start: 0.6084 (Cg_exo) cc_final: 0.5833 (Cg_endo) REVERT: A 409 GLN cc_start: 0.5503 (OUTLIER) cc_final: 0.3988 (tt0) REVERT: A 480 CYS cc_start: 0.1767 (OUTLIER) cc_final: 0.1415 (p) REVERT: A 580 GLN cc_start: 0.4882 (OUTLIER) cc_final: 0.4340 (mp10) REVERT: A 697 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: A 773 GLU cc_start: 0.8287 (tp30) cc_final: 0.8082 (tt0) REVERT: A 900 MET cc_start: 0.8455 (mtp) cc_final: 0.8182 (mtp) REVERT: A 904 TYR cc_start: 0.7497 (m-80) cc_final: 0.7182 (m-80) REVERT: A 979 ASP cc_start: 0.7872 (m-30) cc_final: 0.6798 (t0) REVERT: C 104 TRP cc_start: 0.6777 (m-90) cc_final: 0.6460 (m-90) REVERT: C 271 GLN cc_start: 0.8686 (tt0) cc_final: 0.8306 (mt0) REVERT: C 335 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6847 (pp) REVERT: C 354 ASN cc_start: 0.6416 (OUTLIER) cc_final: 0.6166 (t0) REVERT: C 356 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7218 (tptt) REVERT: C 388 ASN cc_start: 0.7235 (p0) cc_final: 0.6802 (p0) REVERT: C 525 CYS cc_start: 0.5402 (p) cc_final: 0.5123 (t) REVERT: C 532 ASN cc_start: 0.8516 (t0) cc_final: 0.8281 (t0) REVERT: C 537 LYS cc_start: 0.6886 (tmtt) cc_final: 0.6674 (tttp) REVERT: C 747 THR cc_start: 0.7926 (t) cc_final: 0.7465 (m) REVERT: C 751 ASN cc_start: 0.8414 (m-40) cc_final: 0.8031 (m110) REVERT: C 759 PHE cc_start: 0.7865 (t80) cc_final: 0.6996 (t80) REVERT: C 918 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: C 950 ASP cc_start: 0.8094 (m-30) cc_final: 0.7855 (m-30) REVERT: C 1141 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7792 (tt) outliers start: 100 outliers final: 49 residues processed: 285 average time/residue: 0.1473 time to fit residues: 71.7805 Evaluate side-chains 239 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 171 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 308 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 183 optimal weight: 0.0050 chunk 126 optimal weight: 5.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS A 61 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN C 422 ASN C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.194934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135926 restraints weight = 39879.189| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.17 r_work: 0.3487 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26790 Z= 0.121 Angle : 0.615 9.665 36587 Z= 0.304 Chirality : 0.047 0.332 4246 Planarity : 0.006 0.138 4655 Dihedral : 8.954 89.304 4479 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.78 % Favored : 91.91 % Rotamer: Outliers : 4.02 % Allowed : 23.77 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3237 helix: 1.29 (0.21), residues: 678 sheet: -0.40 (0.21), residues: 561 loop : -2.36 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 403 TYR 0.018 0.001 TYR A 904 PHE 0.014 0.001 PHE A 186 TRP 0.015 0.001 TRP B 886 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00278 (26710) covalent geometry : angle 0.59807 (36380) SS BOND : bond 0.00336 ( 33) SS BOND : angle 1.32897 ( 66) hydrogen bonds : bond 0.03869 ( 803) hydrogen bonds : angle 5.38974 ( 2313) link_BETA1-4 : bond 0.00243 ( 12) link_BETA1-4 : angle 1.41967 ( 36) link_NAG-ASN : bond 0.00532 ( 35) link_NAG-ASN : angle 2.49070 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 196 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5429 (mt) REVERT: B 198 ASP cc_start: 0.4674 (OUTLIER) cc_final: 0.4274 (m-30) REVERT: B 374 PHE cc_start: 0.4504 (OUTLIER) cc_final: 0.4285 (m-10) REVERT: B 396 TYR cc_start: 0.6354 (m-80) cc_final: 0.5648 (m-80) REVERT: B 517 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6672 (mp) REVERT: B 580 GLN cc_start: 0.4823 (OUTLIER) cc_final: 0.4494 (mm-40) REVERT: B 592 PHE cc_start: 0.6336 (t80) cc_final: 0.6091 (t80) REVERT: B 751 ASN cc_start: 0.8321 (m-40) cc_final: 0.8039 (m110) REVERT: B 950 ASP cc_start: 0.7925 (m-30) cc_final: 0.7406 (m-30) REVERT: B 964 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8429 (mtmm) REVERT: A 337 PRO cc_start: 0.6241 (Cg_exo) cc_final: 0.5965 (Cg_endo) REVERT: A 356 LYS cc_start: 0.7213 (mmtt) cc_final: 0.7003 (mmtt) REVERT: A 409 GLN cc_start: 0.5438 (OUTLIER) cc_final: 0.3869 (tt0) REVERT: A 480 CYS cc_start: 0.1891 (OUTLIER) cc_final: 0.1526 (p) REVERT: A 529 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6909 (pttm) REVERT: A 580 GLN cc_start: 0.4831 (OUTLIER) cc_final: 0.4339 (mp10) REVERT: A 637 SER cc_start: 0.3647 (OUTLIER) cc_final: 0.3344 (p) REVERT: A 904 TYR cc_start: 0.7235 (m-80) cc_final: 0.6954 (m-80) REVERT: A 979 ASP cc_start: 0.7766 (m-30) cc_final: 0.6678 (t0) REVERT: C 271 GLN cc_start: 0.8588 (tt0) cc_final: 0.8190 (mt0) REVERT: C 321 GLN cc_start: 0.7430 (mm110) cc_final: 0.7037 (mp10) REVERT: C 335 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6861 (pp) REVERT: C 388 ASN cc_start: 0.7122 (p0) cc_final: 0.6699 (p0) REVERT: C 525 CYS cc_start: 0.5084 (p) cc_final: 0.4802 (t) REVERT: C 747 THR cc_start: 0.7872 (t) cc_final: 0.7389 (m) REVERT: C 751 ASN cc_start: 0.8338 (m-40) cc_final: 0.7984 (m110) REVERT: C 759 PHE cc_start: 0.7769 (t80) cc_final: 0.6886 (t80) REVERT: C 918 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7572 (pm20) outliers start: 114 outliers final: 66 residues processed: 292 average time/residue: 0.1449 time to fit residues: 72.1128 Evaluate side-chains 248 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 170 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A 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 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 422 ASN B 487 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1101 HIS A 49 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119010 restraints weight = 40151.279| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.68 r_work: 0.3335 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 26790 Z= 0.431 Angle : 0.929 12.162 36587 Z= 0.466 Chirality : 0.059 0.393 4246 Planarity : 0.007 0.139 4655 Dihedral : 9.256 91.763 4479 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.35 % Favored : 89.37 % Rotamer: Outliers : 5.71 % Allowed : 22.22 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3237 helix: 0.67 (0.21), residues: 678 sheet: -0.78 (0.20), residues: 606 loop : -2.62 (0.12), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 214 TYR 0.038 0.003 TYR A 904 PHE 0.030 0.003 PHE A 927 TRP 0.018 0.003 TRP C 436 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01050 (26710) covalent geometry : angle 0.90363 (36380) SS BOND : bond 0.00849 ( 33) SS BOND : angle 2.57212 ( 66) hydrogen bonds : bond 0.06496 ( 803) hydrogen bonds : angle 6.09504 ( 2313) link_BETA1-4 : bond 0.00394 ( 12) link_BETA1-4 : angle 1.88422 ( 36) link_NAG-ASN : bond 0.00978 ( 35) link_NAG-ASN : angle 3.54975 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 214 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 517 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 580 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4934 (mm-40) REVERT: B 663 ASP cc_start: 0.8507 (t0) cc_final: 0.8297 (t0) REVERT: B 751 ASN cc_start: 0.8563 (m-40) cc_final: 0.8248 (m-40) REVERT: B 820 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8614 (m-30) REVERT: B 904 TYR cc_start: 0.7976 (t80) cc_final: 0.7705 (t80) REVERT: B 994 ASP cc_start: 0.8886 (t70) cc_final: 0.8662 (t0) REVERT: A 78 ARG cc_start: 0.3268 (OUTLIER) cc_final: 0.2080 (mtm-85) REVERT: A 480 CYS cc_start: 0.1439 (OUTLIER) cc_final: 0.1015 (p) REVERT: A 540 ASN cc_start: 0.7682 (m-40) cc_final: 0.6959 (t0) REVERT: A 637 SER cc_start: 0.3810 (OUTLIER) cc_final: 0.3276 (p) REVERT: A 645 THR cc_start: 0.8914 (m) cc_final: 0.8575 (p) REVERT: A 765 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8304 (mtm-85) REVERT: C 65 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6754 (m-10) REVERT: C 96 GLU cc_start: 0.5483 (mt-10) cc_final: 0.5171 (mt-10) REVERT: C 118 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6316 (mm) REVERT: C 170 TYR cc_start: 0.7489 (t80) cc_final: 0.6943 (m-80) REVERT: C 207 HIS cc_start: 0.7679 (m170) cc_final: 0.7471 (m170) REVERT: C 321 GLN cc_start: 0.7780 (mm110) cc_final: 0.7579 (mm-40) REVERT: C 335 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6926 (pp) REVERT: C 356 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7407 (mmtm) REVERT: C 388 ASN cc_start: 0.7245 (p0) cc_final: 0.6818 (p0) REVERT: C 456 PHE cc_start: 0.1503 (OUTLIER) cc_final: 0.1003 (p90) REVERT: C 540 ASN cc_start: 0.7823 (m110) cc_final: 0.7181 (t0) REVERT: C 747 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7608 (m) REVERT: C 751 ASN cc_start: 0.8663 (m-40) cc_final: 0.8267 (m110) REVERT: C 752 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 820 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: C 950 ASP cc_start: 0.7960 (m-30) cc_final: 0.7615 (m-30) REVERT: C 979 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7637 (t70) REVERT: C 994 ASP cc_start: 0.8746 (t70) cc_final: 0.8414 (t0) REVERT: C 1144 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7804 (mm-30) outliers start: 162 outliers final: 91 residues processed: 356 average time/residue: 0.1496 time to fit residues: 91.1674 Evaluate side-chains 288 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 181 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 294 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.182422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121634 restraints weight = 39713.237| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.78 r_work: 0.3378 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26790 Z= 0.178 Angle : 0.698 9.416 36587 Z= 0.347 Chirality : 0.048 0.311 4246 Planarity : 0.006 0.138 4655 Dihedral : 8.078 90.705 4479 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.97 % Favored : 91.78 % Rotamer: Outliers : 4.34 % Allowed : 24.55 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.14), residues: 3237 helix: 0.91 (0.21), residues: 684 sheet: -0.78 (0.19), residues: 645 loop : -2.47 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 319 TYR 0.021 0.001 TYR A 904 PHE 0.022 0.002 PHE B 220 TRP 0.018 0.002 TRP C 633 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00421 (26710) covalent geometry : angle 0.67502 (36380) SS BOND : bond 0.00448 ( 33) SS BOND : angle 1.85416 ( 66) hydrogen bonds : bond 0.04626 ( 803) hydrogen bonds : angle 5.62842 ( 2313) link_BETA1-4 : bond 0.00212 ( 12) link_BETA1-4 : angle 1.42735 ( 36) link_NAG-ASN : bond 0.00559 ( 35) link_NAG-ASN : angle 2.99976 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 203 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7711 (mmm-85) REVERT: B 517 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 564 GLN cc_start: 0.7013 (mm110) cc_final: 0.6566 (mt0) REVERT: B 580 GLN cc_start: 0.5203 (OUTLIER) cc_final: 0.4796 (mm-40) REVERT: B 751 ASN cc_start: 0.8575 (m-40) cc_final: 0.8314 (m-40) REVERT: B 1002 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8276 (tp40) REVERT: A 78 ARG cc_start: 0.2832 (OUTLIER) cc_final: 0.1703 (mtm-85) REVERT: A 329 PHE cc_start: 0.6249 (m-10) cc_final: 0.5874 (m-10) REVERT: A 356 LYS cc_start: 0.7144 (mptt) cc_final: 0.6883 (mmtt) REVERT: A 529 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7114 (pttm) REVERT: A 540 ASN cc_start: 0.7652 (m-40) cc_final: 0.7289 (t0) REVERT: A 637 SER cc_start: 0.3571 (OUTLIER) cc_final: 0.3048 (p) REVERT: A 645 THR cc_start: 0.8875 (m) cc_final: 0.8572 (p) REVERT: A 904 TYR cc_start: 0.7511 (m-80) cc_final: 0.7155 (m-80) REVERT: A 979 ASP cc_start: 0.7988 (m-30) cc_final: 0.6776 (t0) REVERT: C 65 PHE cc_start: 0.7024 (m-10) cc_final: 0.6815 (m-10) REVERT: C 96 GLU cc_start: 0.5439 (mt-10) cc_final: 0.4974 (mt-10) REVERT: C 170 TYR cc_start: 0.7327 (t80) cc_final: 0.6835 (m-80) REVERT: C 207 HIS cc_start: 0.7677 (m170) cc_final: 0.7410 (m170) REVERT: C 388 ASN cc_start: 0.7149 (p0) cc_final: 0.6679 (p0) REVERT: C 540 ASN cc_start: 0.7648 (m110) cc_final: 0.7040 (t0) REVERT: C 747 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7526 (m) REVERT: C 751 ASN cc_start: 0.8672 (m-40) cc_final: 0.8257 (m110) REVERT: C 765 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7924 (mtm-85) REVERT: C 994 ASP cc_start: 0.8702 (t70) cc_final: 0.8370 (t0) REVERT: C 1144 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8223 (tp30) outliers start: 123 outliers final: 79 residues processed: 307 average time/residue: 0.1352 time to fit residues: 71.1268 Evaluate side-chains 271 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 184 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 109 optimal weight: 0.0980 chunk 129 optimal weight: 0.2980 chunk 215 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125111 restraints weight = 39469.537| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.84 r_work: 0.3395 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26790 Z= 0.114 Angle : 0.637 14.249 36587 Z= 0.315 Chirality : 0.046 0.312 4246 Planarity : 0.006 0.136 4655 Dihedral : 7.157 87.538 4479 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.50 % Favored : 91.29 % Rotamer: Outliers : 3.28 % Allowed : 25.64 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.14), residues: 3237 helix: 1.34 (0.21), residues: 675 sheet: -0.70 (0.18), residues: 681 loop : -2.44 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.016 0.001 TYR B 396 PHE 0.019 0.001 PHE C 392 TRP 0.019 0.001 TRP B 886 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00254 (26710) covalent geometry : angle 0.61699 (36380) SS BOND : bond 0.00375 ( 33) SS BOND : angle 1.60457 ( 66) hydrogen bonds : bond 0.03806 ( 803) hydrogen bonds : angle 5.29898 ( 2313) link_BETA1-4 : bond 0.00232 ( 12) link_BETA1-4 : angle 1.49879 ( 36) link_NAG-ASN : bond 0.00554 ( 35) link_NAG-ASN : angle 2.69371 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 203 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 GLN cc_start: 0.6847 (mm110) cc_final: 0.6467 (mt0) REVERT: B 580 GLN cc_start: 0.5060 (OUTLIER) cc_final: 0.4652 (mm-40) REVERT: B 751 ASN cc_start: 0.8528 (m-40) cc_final: 0.8323 (m-40) REVERT: B 755 GLN cc_start: 0.8796 (tt0) cc_final: 0.8566 (tt0) REVERT: A 191 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7177 (mm-30) REVERT: A 356 LYS cc_start: 0.6966 (mptt) cc_final: 0.6760 (mmtt) REVERT: A 387 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.6085 (mp) REVERT: A 512 VAL cc_start: 0.7148 (t) cc_final: 0.6885 (m) REVERT: A 529 LYS cc_start: 0.7436 (mmmt) cc_final: 0.7033 (pttm) REVERT: A 540 ASN cc_start: 0.7509 (m-40) cc_final: 0.6780 (t0) REVERT: A 637 SER cc_start: 0.3219 (OUTLIER) cc_final: 0.2741 (p) REVERT: A 645 THR cc_start: 0.8848 (m) cc_final: 0.8482 (p) REVERT: A 904 TYR cc_start: 0.7431 (m-80) cc_final: 0.7140 (m-80) REVERT: C 96 GLU cc_start: 0.5098 (mt-10) cc_final: 0.4739 (mt-10) REVERT: C 170 TYR cc_start: 0.7239 (t80) cc_final: 0.6784 (m-80) REVERT: C 190 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6226 (mmt90) REVERT: C 388 ASN cc_start: 0.7160 (p0) cc_final: 0.6677 (p0) REVERT: C 540 ASN cc_start: 0.7587 (m110) cc_final: 0.6918 (t0) REVERT: C 564 GLN cc_start: 0.7075 (mm110) cc_final: 0.6640 (mt0) REVERT: C 596 SER cc_start: 0.9318 (t) cc_final: 0.8868 (m) REVERT: C 747 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7505 (m) REVERT: C 751 ASN cc_start: 0.8580 (m-40) cc_final: 0.8153 (m110) REVERT: C 979 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7482 (t0) outliers start: 93 outliers final: 68 residues processed: 279 average time/residue: 0.1465 time to fit residues: 70.3253 Evaluate side-chains 259 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 171 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 255 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 189 optimal weight: 0.2980 chunk 254 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 299 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.183702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123372 restraints weight = 39635.011| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.91 r_work: 0.3386 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26790 Z= 0.126 Angle : 0.625 9.575 36587 Z= 0.310 Chirality : 0.046 0.319 4246 Planarity : 0.006 0.137 4655 Dihedral : 6.707 84.447 4479 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.16 % Favored : 91.63 % Rotamer: Outliers : 3.60 % Allowed : 25.01 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3237 helix: 1.43 (0.21), residues: 675 sheet: -0.62 (0.19), residues: 681 loop : -2.37 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.017 0.001 TYR A 904 PHE 0.019 0.001 PHE C 392 TRP 0.014 0.001 TRP C 633 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00292 (26710) covalent geometry : angle 0.60512 (36380) SS BOND : bond 0.00355 ( 33) SS BOND : angle 1.67399 ( 66) hydrogen bonds : bond 0.03835 ( 803) hydrogen bonds : angle 5.16825 ( 2313) link_BETA1-4 : bond 0.00255 ( 12) link_BETA1-4 : angle 1.41689 ( 36) link_NAG-ASN : bond 0.00538 ( 35) link_NAG-ASN : angle 2.61314 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 188 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 GLN cc_start: 0.6901 (mm110) cc_final: 0.6551 (mt0) REVERT: B 580 GLN cc_start: 0.5474 (OUTLIER) cc_final: 0.5033 (mm-40) REVERT: B 751 ASN cc_start: 0.8527 (m-40) cc_final: 0.8264 (m110) REVERT: A 191 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7243 (mm-30) REVERT: A 356 LYS cc_start: 0.6803 (mptt) cc_final: 0.6595 (mmtt) REVERT: A 387 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6164 (mp) REVERT: A 512 VAL cc_start: 0.7262 (t) cc_final: 0.6973 (m) REVERT: A 529 LYS cc_start: 0.7414 (mmmt) cc_final: 0.7006 (pttm) REVERT: A 540 ASN cc_start: 0.7546 (m-40) cc_final: 0.6886 (t0) REVERT: A 637 SER cc_start: 0.3277 (OUTLIER) cc_final: 0.2814 (p) REVERT: A 904 TYR cc_start: 0.7576 (m-80) cc_final: 0.7211 (m-80) REVERT: C 96 GLU cc_start: 0.5053 (mt-10) cc_final: 0.4679 (mt-10) REVERT: C 170 TYR cc_start: 0.7446 (t80) cc_final: 0.6893 (m-80) REVERT: C 190 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6171 (mmt90) REVERT: C 356 LYS cc_start: 0.7326 (mmtt) cc_final: 0.6902 (mmtm) REVERT: C 388 ASN cc_start: 0.7152 (p0) cc_final: 0.6683 (p0) REVERT: C 540 ASN cc_start: 0.7485 (m110) cc_final: 0.6838 (t0) REVERT: C 560 LEU cc_start: 0.5922 (mm) cc_final: 0.5615 (mt) REVERT: C 564 GLN cc_start: 0.7173 (mm110) cc_final: 0.6849 (mt0) REVERT: C 747 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7473 (m) REVERT: C 751 ASN cc_start: 0.8542 (m-40) cc_final: 0.8101 (m110) REVERT: C 765 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7704 (mtm-85) REVERT: C 979 ASP cc_start: 0.8154 (m-30) cc_final: 0.7551 (t70) outliers start: 102 outliers final: 77 residues processed: 277 average time/residue: 0.1459 time to fit residues: 70.0652 Evaluate side-chains 265 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 182 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 144 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 271 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1054 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.178443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121250 restraints weight = 39669.589| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.72 r_work: 0.3312 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26790 Z= 0.242 Angle : 0.721 10.491 36587 Z= 0.360 Chirality : 0.050 0.319 4246 Planarity : 0.006 0.139 4655 Dihedral : 7.015 83.006 4479 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.95 % Favored : 89.87 % Rotamer: Outliers : 3.77 % Allowed : 24.69 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3237 helix: 1.19 (0.21), residues: 678 sheet: -0.62 (0.19), residues: 645 loop : -2.46 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 319 TYR 0.026 0.002 TYR A 904 PHE 0.020 0.002 PHE A 898 TRP 0.016 0.002 TRP B 886 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00582 (26710) covalent geometry : angle 0.69816 (36380) SS BOND : bond 0.00459 ( 33) SS BOND : angle 2.13820 ( 66) hydrogen bonds : bond 0.05003 ( 803) hydrogen bonds : angle 5.43685 ( 2313) link_BETA1-4 : bond 0.00336 ( 12) link_BETA1-4 : angle 1.46304 ( 36) link_NAG-ASN : bond 0.00625 ( 35) link_NAG-ASN : angle 2.94654 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 190 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7803 (mmm-85) REVERT: B 517 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6937 (mp) REVERT: B 529 LYS cc_start: 0.6856 (mptt) cc_final: 0.6034 (tttm) REVERT: B 564 GLN cc_start: 0.7067 (mm110) cc_final: 0.6756 (mt0) REVERT: B 748 GLU cc_start: 0.8089 (pm20) cc_final: 0.7870 (pm20) REVERT: B 751 ASN cc_start: 0.8640 (m-40) cc_final: 0.8420 (m-40) REVERT: B 755 GLN cc_start: 0.8881 (tt0) cc_final: 0.8590 (tt0) REVERT: A 65 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.5877 (m-10) REVERT: A 356 LYS cc_start: 0.6971 (mptt) cc_final: 0.6748 (mmtt) REVERT: A 387 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6059 (mp) REVERT: A 540 ASN cc_start: 0.7843 (m-40) cc_final: 0.7020 (t0) REVERT: A 637 SER cc_start: 0.3741 (OUTLIER) cc_final: 0.3032 (p) REVERT: A 751 ASN cc_start: 0.8571 (m110) cc_final: 0.8286 (m110) REVERT: A 904 TYR cc_start: 0.7761 (m-80) cc_final: 0.7300 (m-80) REVERT: A 979 ASP cc_start: 0.8064 (m-30) cc_final: 0.6965 (t70) REVERT: C 118 LEU cc_start: 0.6514 (mm) cc_final: 0.6255 (mm) REVERT: C 170 TYR cc_start: 0.7537 (t80) cc_final: 0.7016 (m-80) REVERT: C 190 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6191 (mmt90) REVERT: C 356 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6907 (mmtm) REVERT: C 388 ASN cc_start: 0.7215 (p0) cc_final: 0.6737 (p0) REVERT: C 525 CYS cc_start: 0.6354 (p) cc_final: 0.5675 (p) REVERT: C 540 ASN cc_start: 0.7593 (m-40) cc_final: 0.6965 (t0) REVERT: C 560 LEU cc_start: 0.6127 (mm) cc_final: 0.5783 (mt) REVERT: C 564 GLN cc_start: 0.7390 (mm110) cc_final: 0.7036 (mt0) REVERT: C 747 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7419 (m) REVERT: C 751 ASN cc_start: 0.8678 (m-40) cc_final: 0.8234 (m110) REVERT: C 765 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7927 (mtm-85) outliers start: 107 outliers final: 84 residues processed: 280 average time/residue: 0.1563 time to fit residues: 74.1921 Evaluate side-chains 267 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 176 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 83 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 152 optimal weight: 0.2980 chunk 250 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.180552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119865 restraints weight = 39547.206| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.66 r_work: 0.3362 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26790 Z= 0.146 Angle : 0.657 10.788 36587 Z= 0.327 Chirality : 0.047 0.302 4246 Planarity : 0.006 0.143 4655 Dihedral : 6.744 83.095 4479 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.25 % Favored : 91.57 % Rotamer: Outliers : 3.32 % Allowed : 25.40 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3237 helix: 1.12 (0.21), residues: 696 sheet: -0.63 (0.19), residues: 699 loop : -2.40 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.019 0.001 TYR A 904 PHE 0.017 0.001 PHE C 562 TRP 0.014 0.001 TRP A 633 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00343 (26710) covalent geometry : angle 0.63653 (36380) SS BOND : bond 0.00404 ( 33) SS BOND : angle 1.78155 ( 66) hydrogen bonds : bond 0.04185 ( 803) hydrogen bonds : angle 5.29132 ( 2313) link_BETA1-4 : bond 0.00410 ( 12) link_BETA1-4 : angle 1.26656 ( 36) link_NAG-ASN : bond 0.00540 ( 35) link_NAG-ASN : angle 2.74499 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6474 Ramachandran restraints generated. 3237 Oldfield, 0 Emsley, 3237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 179 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 529 LYS cc_start: 0.6870 (mptt) cc_final: 0.6383 (pttm) REVERT: B 564 GLN cc_start: 0.7009 (mm110) cc_final: 0.6761 (mt0) REVERT: B 748 GLU cc_start: 0.8014 (pm20) cc_final: 0.7772 (pm20) REVERT: B 751 ASN cc_start: 0.8579 (m-40) cc_final: 0.8334 (m110) REVERT: B 755 GLN cc_start: 0.8810 (tt0) cc_final: 0.8541 (tt0) REVERT: A 65 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.5755 (m-10) REVERT: A 78 ARG cc_start: 0.2851 (OUTLIER) cc_final: 0.1563 (mtm-85) REVERT: A 356 LYS cc_start: 0.6924 (mptt) cc_final: 0.6688 (mmtt) REVERT: A 387 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5916 (mp) REVERT: A 540 ASN cc_start: 0.7809 (m-40) cc_final: 0.7017 (t0) REVERT: A 637 SER cc_start: 0.3724 (OUTLIER) cc_final: 0.3013 (p) REVERT: A 645 THR cc_start: 0.8852 (m) cc_final: 0.8489 (p) REVERT: A 751 ASN cc_start: 0.8547 (m110) cc_final: 0.8274 (m-40) REVERT: A 904 TYR cc_start: 0.7559 (m-80) cc_final: 0.7198 (m-80) REVERT: C 170 TYR cc_start: 0.7435 (t80) cc_final: 0.7036 (m-80) REVERT: C 190 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6235 (mmt90) REVERT: C 356 LYS cc_start: 0.7341 (mmtt) cc_final: 0.6875 (mmtm) REVERT: C 388 ASN cc_start: 0.7164 (p0) cc_final: 0.6688 (p0) REVERT: C 525 CYS cc_start: 0.6543 (p) cc_final: 0.5817 (p) REVERT: C 540 ASN cc_start: 0.7607 (m-40) cc_final: 0.7023 (t0) REVERT: C 560 LEU cc_start: 0.6082 (mm) cc_final: 0.5753 (mt) REVERT: C 564 GLN cc_start: 0.7457 (mm110) cc_final: 0.7160 (mt0) REVERT: C 747 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7405 (m) REVERT: C 751 ASN cc_start: 0.8649 (m-40) cc_final: 0.8212 (m110) outliers start: 94 outliers final: 79 residues processed: 259 average time/residue: 0.1524 time to fit residues: 67.6272 Evaluate side-chains 261 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 176 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 296 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 263 optimal weight: 0.0670 chunk 304 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 129 optimal weight: 0.0370 chunk 134 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.186129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127982 restraints weight = 39889.829| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.86 r_work: 0.3399 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 26790 Z= 0.117 Angle : 0.627 10.614 36587 Z= 0.311 Chirality : 0.046 0.302 4246 Planarity : 0.006 0.144 4655 Dihedral : 6.437 81.400 4479 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.50 % Favored : 91.35 % Rotamer: Outliers : 3.07 % Allowed : 25.68 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3237 helix: 1.13 (0.21), residues: 717 sheet: -0.47 (0.19), residues: 669 loop : -2.32 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.018 0.001 TYR B 396 PHE 0.016 0.001 PHE C 562 TRP 0.014 0.001 TRP A 633 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (26710) covalent geometry : angle 0.60834 (36380) SS BOND : bond 0.00349 ( 33) SS BOND : angle 1.57266 ( 66) hydrogen bonds : bond 0.03775 ( 803) hydrogen bonds : angle 5.12225 ( 2313) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 1.21697 ( 36) link_NAG-ASN : bond 0.00536 ( 35) link_NAG-ASN : angle 2.60171 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9605.56 seconds wall clock time: 164 minutes 14.84 seconds (9854.84 seconds total)