Starting phenix.real_space_refine on Sun Jul 5 07:03:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xiy_33212/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.map" model { file = "/net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xiy_33212/07_2026/7xiy_33212.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 8 Time building chain proxies: 5.43, per 1000 atoms: 0.21 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 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: 0.78 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: 4.92 Time building geometry restraints manager: 2.43 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 - 18.02: 13192 18.02 - 36.04: 1780 36.04 - 54.05: 409 54.05 - 72.07: 79 72.07 - 90.09: 44 Dihedral angle restraints: 15504 sinusoidal: 6021 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 15501 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.750 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 17.520 90.090 9309 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/Z covalent geometry : bond 0.00589 / 0.24 (26710) covalent geometry : angle 0.85715 / 0.46 (36380) SS BOND : bond 0.00335 / 0.23 ( 33) SS BOND : angle 1.36839 / 0.89 ( 66) hydrogen bonds : bond 0.21295 / 13.86 ( 803) hydrogen bonds : angle 8.20493 / 5.57 ( 2313) link_BETA1-4 : bond 0.00392 / 0.26 ( 12) link_BETA1-4 : angle 1.28862 / 0.89 ( 36) link_NAG-ASN : bond 0.00795 / 0.51 ( 35) link_NAG-ASN : angle 2.84408 / 2.09 ( 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 : 0.962 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: 0.1604 time to fit residues: 105.0442 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 : 0.693 ------------------------------------------------------------------------------- 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... ** 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 675 GLN C 901 GLN C 955 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.197249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135377 restraints weight = 40406.759| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.97 r_work: 0.3543 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26790 Z= 0.160 Angle : 0.663 10.006 36587 Z= 0.338 Chirality : 0.048 0.329 4246 Planarity : 0.006 0.142 4655 Dihedral : 4.939 42.863 3495 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.57 % Favored : 92.09 % Rotamer: Outliers : 3.70 % Allowed : 24.73 % Favored : 71.57 % 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: -2.04 (0.14), residues: 3237 helix: 0.75 (0.20), residues: 678 sheet: -0.67 (0.21), residues: 570 loop : -2.48 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 567 TYR 0.025 0.002 TYR A 904 PHE 0.022 0.002 PHE C 338 TRP 0.019 0.002 TRP A 633 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (26710) covalent geometry : angle 0.64675 / 0.33 (36380) SS BOND : bond 0.00424 / 0.28 ( 33) SS BOND : angle 1.59065 / 1.09 ( 66) hydrogen bonds : bond 0.04544 / 2.95 ( 803) hydrogen bonds : angle 5.95260 / 4.06 ( 2313) link_BETA1-4 : bond 0.00399 / 0.25 ( 12) link_BETA1-4 : angle 1.15694 / 0.76 ( 36) link_NAG-ASN : bond 0.00556 / 0.35 ( 35) link_NAG-ASN : angle 2.50930 / 1.79 ( 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 318 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 213 time to evaluate : 0.942 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: 0.4957 (t70) cc_final: 0.4715 (t70) REVERT: B 337 PRO cc_start: 0.6498 (Cg_exo) cc_final: 0.5938 (Cg_endo) REVERT: B 663 ASP cc_start: 0.7357 (t0) cc_final: 0.7127 (t0) REVERT: B 751 ASN cc_start: 0.8420 (m-40) cc_final: 0.8122 (m-40) REVERT: B 950 ASP cc_start: 0.7963 (m-30) cc_final: 0.7427 (m-30) REVERT: B 964 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8387 (mtmm) REVERT: A 409 GLN cc_start: 0.5635 (OUTLIER) cc_final: 0.3970 (tt0) REVERT: A 580 GLN cc_start: 0.4647 (OUTLIER) cc_final: 0.4249 (mp10) REVERT: A 645 THR cc_start: 0.8745 (m) cc_final: 0.8468 (p) REVERT: A 697 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7924 (mtp) REVERT: A 979 ASP cc_start: 0.7682 (m-30) cc_final: 0.6613 (t0) REVERT: C 104 TRP cc_start: 0.6632 (m-90) cc_final: 0.6189 (m-90) REVERT: C 271 GLN cc_start: 0.8624 (tt0) cc_final: 0.8229 (mt0) REVERT: C 321 GLN cc_start: 0.7550 (mm110) cc_final: 0.7159 (mp10) REVERT: C 335 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6835 (pp) REVERT: C 388 ASN cc_start: 0.7150 (p0) cc_final: 0.6647 (p0) REVERT: C 525 CYS cc_start: 0.5549 (p) cc_final: 0.5245 (t) REVERT: C 537 LYS cc_start: 0.6753 (tmtt) cc_final: 0.6513 (tttp) REVERT: C 565 PHE cc_start: 0.6826 (m-10) cc_final: 0.6620 (m-10) REVERT: C 747 THR cc_start: 0.7918 (t) cc_final: 0.7399 (m) REVERT: C 751 ASN cc_start: 0.8269 (m-40) cc_final: 0.7907 (m-40) REVERT: C 759 PHE cc_start: 0.7662 (t80) cc_final: 0.6666 (t80) REVERT: C 918 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: C 950 ASP cc_start: 0.7851 (m-30) cc_final: 0.7638 (m-30) outliers start: 105 outliers final: 41 residues processed: 301 average time/residue: 0.1480 time to fit residues: 75.0926 Evaluate side-chains 223 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 791 THR Chi-restraints excluded: chain B residue 859 THR 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 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: 0.7980 chunk 172 optimal weight: 0.7980 chunk 287 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 318 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.196674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136106 restraints weight = 40357.809| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.74 r_work: 0.3559 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26790 Z= 0.115 Angle : 0.603 12.015 36587 Z= 0.303 Chirality : 0.046 0.314 4246 Planarity : 0.006 0.139 4655 Dihedral : 4.706 42.419 3492 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.20 % Favored : 92.49 % Rotamer: Outliers : 3.17 % Allowed : 24.30 % Favored : 72.52 % 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: 1.14 (0.21), residues: 675 sheet: -0.40 (0.21), residues: 561 loop : -2.37 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 567 TYR 0.019 0.001 TYR A 904 PHE 0.014 0.001 PHE B 338 TRP 0.015 0.001 TRP C 633 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (26710) covalent geometry : angle 0.58907 / 0.30 (36380) SS BOND : bond 0.00339 / 0.21 ( 33) SS BOND : angle 1.27771 / 0.89 ( 66) hydrogen bonds : bond 0.04183 / 2.73 ( 803) hydrogen bonds : angle 5.55992 / 3.80 ( 2313) link_BETA1-4 : bond 0.00323 / 0.21 ( 12) link_BETA1-4 : angle 1.00371 / 0.70 ( 36) link_NAG-ASN : bond 0.00592 / 0.38 ( 35) link_NAG-ASN : angle 2.21240 / 1.63 ( 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 286 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5524 (mt) REVERT: B 337 PRO cc_start: 0.6373 (Cg_exo) cc_final: 0.6092 (Cg_endo) REVERT: B 374 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4338 (t80) REVERT: B 751 ASN cc_start: 0.8436 (m-40) cc_final: 0.8146 (m-40) REVERT: B 912 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 950 ASP cc_start: 0.8140 (m-30) cc_final: 0.7578 (m-30) REVERT: B 964 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8474 (mtmm) REVERT: B 994 ASP cc_start: 0.8698 (t70) cc_final: 0.8418 (t0) REVERT: A 337 PRO cc_start: 0.6135 (Cg_exo) cc_final: 0.5883 (Cg_endo) REVERT: A 409 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.3990 (tt0) REVERT: A 480 CYS cc_start: 0.1771 (OUTLIER) cc_final: 0.1427 (p) REVERT: A 580 GLN cc_start: 0.4839 (OUTLIER) cc_final: 0.4302 (mp10) REVERT: A 697 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: A 950 ASP cc_start: 0.8066 (m-30) cc_final: 0.7773 (m-30) REVERT: A 979 ASP cc_start: 0.7843 (m-30) cc_final: 0.6784 (t0) REVERT: C 271 GLN cc_start: 0.8645 (tt0) cc_final: 0.8274 (mt0) REVERT: C 335 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6828 (pp) REVERT: C 354 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.6160 (t0) REVERT: C 356 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7280 (tptt) REVERT: C 388 ASN cc_start: 0.7202 (p0) cc_final: 0.6767 (p0) REVERT: C 525 CYS cc_start: 0.5606 (p) cc_final: 0.5382 (t) REVERT: C 532 ASN cc_start: 0.8458 (t0) cc_final: 0.8239 (t0) REVERT: C 537 LYS cc_start: 0.6873 (tmtt) cc_final: 0.6627 (tttp) REVERT: C 747 THR cc_start: 0.7881 (t) cc_final: 0.7417 (m) REVERT: C 751 ASN cc_start: 0.8393 (m-40) cc_final: 0.8015 (m110) REVERT: C 759 PHE cc_start: 0.7803 (t80) cc_final: 0.6969 (t80) REVERT: C 918 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: C 950 ASP cc_start: 0.8046 (m-30) cc_final: 0.7821 (m-30) REVERT: C 1141 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7774 (tt) outliers start: 90 outliers final: 43 residues processed: 275 average time/residue: 0.1540 time to fit residues: 71.9917 Evaluate side-chains 232 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 A residue 63 THR 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 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 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: 0.9980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 308 optimal weight: 0.0980 chunk 257 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.197686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140276 restraints weight = 40493.997| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.79 r_work: 0.3544 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 26790 Z= 0.110 Angle : 0.584 9.965 36587 Z= 0.295 Chirality : 0.046 0.312 4246 Planarity : 0.006 0.138 4655 Dihedral : 4.578 40.196 3492 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.66 % Favored : 92.03 % Rotamer: Outliers : 3.63 % Allowed : 24.23 % Favored : 72.13 % 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: -1.61 (0.14), residues: 3237 helix: 1.47 (0.21), residues: 663 sheet: -0.39 (0.21), residues: 561 loop : -2.32 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 567 TYR 0.018 0.001 TYR A 904 PHE 0.013 0.001 PHE C 565 TRP 0.015 0.001 TRP C 633 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (26710) covalent geometry : angle 0.57059 / 0.29 (36380) SS BOND : bond 0.00425 / 0.24 ( 33) SS BOND : angle 1.25201 / 0.90 ( 66) hydrogen bonds : bond 0.03757 / 2.44 ( 803) hydrogen bonds : angle 5.34809 / 3.68 ( 2313) link_BETA1-4 : bond 0.00309 / 0.20 ( 12) link_BETA1-4 : angle 1.00918 / 0.70 ( 36) link_NAG-ASN : bond 0.00556 / 0.36 ( 35) link_NAG-ASN : angle 2.12211 / 1.57 ( 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 294 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 191 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5487 (mt) REVERT: B 198 ASP cc_start: 0.4760 (OUTLIER) cc_final: 0.4339 (m-30) REVERT: B 337 PRO cc_start: 0.6134 (Cg_exo) cc_final: 0.5569 (Cg_endo) REVERT: B 356 LYS cc_start: 0.7457 (tptt) cc_final: 0.6847 (tptp) REVERT: B 374 PHE cc_start: 0.4589 (OUTLIER) cc_final: 0.4360 (m-10) REVERT: B 396 TYR cc_start: 0.6404 (m-80) cc_final: 0.5625 (m-80) REVERT: B 517 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6749 (mp) REVERT: B 580 GLN cc_start: 0.4819 (OUTLIER) cc_final: 0.4491 (mm-40) REVERT: B 751 ASN cc_start: 0.8367 (m-40) cc_final: 0.8062 (m110) REVERT: B 950 ASP cc_start: 0.8134 (m-30) cc_final: 0.7609 (m-30) REVERT: B 964 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8577 (mtmm) REVERT: A 337 PRO cc_start: 0.6254 (Cg_exo) cc_final: 0.5984 (Cg_endo) REVERT: A 356 LYS cc_start: 0.7292 (mmtt) cc_final: 0.7081 (mmtt) REVERT: A 409 GLN cc_start: 0.5357 (OUTLIER) cc_final: 0.3802 (tt0) REVERT: A 480 CYS cc_start: 0.1821 (OUTLIER) cc_final: 0.1471 (p) REVERT: A 529 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6968 (pttm) REVERT: A 580 GLN cc_start: 0.4783 (OUTLIER) cc_final: 0.4255 (mp10) REVERT: A 979 ASP cc_start: 0.7860 (m-30) cc_final: 0.6807 (t0) REVERT: C 96 GLU cc_start: 0.5507 (mt-10) cc_final: 0.5093 (mt-10) REVERT: C 271 GLN cc_start: 0.8625 (tt0) cc_final: 0.8263 (mt0) REVERT: C 335 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6852 (pp) REVERT: C 388 ASN cc_start: 0.7196 (p0) cc_final: 0.6773 (p0) REVERT: C 525 CYS cc_start: 0.5096 (p) cc_final: 0.4853 (t) REVERT: C 747 THR cc_start: 0.7867 (t) cc_final: 0.7381 (m) REVERT: C 751 ASN cc_start: 0.8417 (m-40) cc_final: 0.8044 (m110) REVERT: C 759 PHE cc_start: 0.7805 (t80) cc_final: 0.6985 (t80) REVERT: C 918 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7760 (pm20) outliers start: 103 outliers final: 57 residues processed: 278 average time/residue: 0.1500 time to fit residues: 71.3955 Evaluate side-chains 236 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 213 VAL Chi-restraints excluded: chain A residue 241 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 395 VAL 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 642 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET 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 916 LEU 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 C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL 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 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 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: 0.9990 chunk 116 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 262 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 901 GLN A 49 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.191418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133231 restraints weight = 39915.957| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.02 r_work: 0.3481 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26790 Z= 0.145 Angle : 0.612 9.712 36587 Z= 0.307 Chirality : 0.047 0.308 4246 Planarity : 0.006 0.136 4655 Dihedral : 4.608 40.966 3492 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.09 % Favored : 91.63 % Rotamer: Outliers : 3.84 % Allowed : 23.70 % Favored : 72.45 % 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: -1.63 (0.14), residues: 3237 helix: 1.32 (0.21), residues: 678 sheet: -0.43 (0.20), residues: 618 loop : -2.35 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.015 0.001 TYR A 904 PHE 0.022 0.001 PHE A 898 TRP 0.014 0.001 TRP B 633 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (26710) covalent geometry : angle 0.59686 / 0.30 (36380) SS BOND : bond 0.00362 / 0.22 ( 33) SS BOND : angle 1.51288 / 1.08 ( 66) hydrogen bonds : bond 0.04067 / 2.64 ( 803) hydrogen bonds : angle 5.26682 / 3.63 ( 2313) link_BETA1-4 : bond 0.00240 / 0.15 ( 12) link_BETA1-4 : angle 1.15939 / 0.80 ( 36) link_NAG-ASN : bond 0.00529 / 0.33 ( 35) link_NAG-ASN : angle 2.31915 / 1.70 ( 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 304 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 195 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.4978 (OUTLIER) cc_final: 0.4405 (m-30) REVERT: B 207 HIS cc_start: 0.7578 (m170) cc_final: 0.7267 (m170) REVERT: B 321 GLN cc_start: 0.7046 (mp10) cc_final: 0.6610 (mp10) REVERT: B 337 PRO cc_start: 0.6099 (Cg_exo) cc_final: 0.5795 (Cg_endo) REVERT: B 374 PHE cc_start: 0.4662 (OUTLIER) cc_final: 0.4377 (m-10) REVERT: B 517 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6836 (mp) REVERT: B 580 GLN cc_start: 0.4851 (OUTLIER) cc_final: 0.4499 (mm-40) REVERT: B 748 GLU cc_start: 0.7979 (pm20) cc_final: 0.7537 (pm20) REVERT: B 912 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 78 ARG cc_start: 0.2408 (OUTLIER) cc_final: 0.1436 (mtm-85) REVERT: A 337 PRO cc_start: 0.6262 (Cg_exo) cc_final: 0.5999 (Cg_endo) REVERT: A 480 CYS cc_start: 0.1876 (OUTLIER) cc_final: 0.1511 (p) REVERT: A 529 LYS cc_start: 0.7182 (mmmt) cc_final: 0.6872 (pttm) REVERT: A 580 GLN cc_start: 0.4741 (OUTLIER) cc_final: 0.4342 (mp10) REVERT: A 637 SER cc_start: 0.3422 (OUTLIER) cc_final: 0.3140 (p) REVERT: A 979 ASP cc_start: 0.7912 (m-30) cc_final: 0.6836 (t0) REVERT: C 96 GLU cc_start: 0.5462 (mt-10) cc_final: 0.5017 (mt-10) REVERT: C 271 GLN cc_start: 0.8627 (tt0) cc_final: 0.8257 (mt0) REVERT: C 335 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7040 (pp) REVERT: C 368 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5200 (mp) REVERT: C 388 ASN cc_start: 0.7311 (p0) cc_final: 0.6847 (p0) REVERT: C 747 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7374 (m) REVERT: C 751 ASN cc_start: 0.8439 (m-40) cc_final: 0.8071 (m110) REVERT: C 918 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: C 950 ASP cc_start: 0.7893 (m-30) cc_final: 0.7662 (m-30) REVERT: C 979 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7253 (t0) outliers start: 109 outliers final: 67 residues processed: 288 average time/residue: 0.1355 time to fit residues: 67.3249 Evaluate side-chains 257 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 176 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 524 VAL 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 660 TYR Chi-restraints excluded: chain B residue 791 THR 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 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 63 THR 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 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR 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 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 740 MET 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 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 124 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 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 368 LEU 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 723 THR Chi-restraints excluded: chain C residue 747 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 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 294 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 751 ASN B1101 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 207 HIS A 409 GLN A 992 GLN ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118703 restraints weight = 40071.185| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.48 r_work: 0.3344 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 26790 Z= 0.398 Angle : 0.918 17.334 36587 Z= 0.459 Chirality : 0.061 1.068 4246 Planarity : 0.008 0.139 4655 Dihedral : 5.844 42.017 3492 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.60 % Favored : 89.16 % Rotamer: Outliers : 5.36 % Allowed : 22.57 % 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: -2.18 (0.14), residues: 3237 helix: 0.64 (0.20), residues: 681 sheet: -0.76 (0.20), residues: 606 loop : -2.62 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG C 190 TYR 0.028 0.003 TYR C 248 PHE 0.031 0.003 PHE A 927 TRP 0.034 0.003 TRP B 886 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00959 / 0.40 (26710) covalent geometry : angle 0.89129 / 0.45 (36380) SS BOND : bond 0.01296 / 0.59 ( 33) SS BOND : angle 2.52180 / 1.73 ( 66) hydrogen bonds : bond 0.06349 / 4.13 ( 803) hydrogen bonds : angle 6.02424 / 4.15 ( 2313) link_BETA1-4 : bond 0.01693 / 1.36 ( 12) link_BETA1-4 : angle 2.45782 / 1.62 ( 36) link_NAG-ASN : bond 0.00802 / 0.48 ( 35) link_NAG-ASN : angle 3.53279 / 2.50 ( 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 360 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 208 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 517 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6994 (mp) REVERT: B 580 GLN cc_start: 0.5264 (OUTLIER) cc_final: 0.5007 (pm20) REVERT: B 697 MET cc_start: 0.8528 (mtp) cc_final: 0.8243 (mtp) REVERT: B 820 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: A 78 ARG cc_start: 0.3303 (OUTLIER) cc_final: 0.1962 (mtm-85) REVERT: A 480 CYS cc_start: 0.1731 (OUTLIER) cc_final: 0.1153 (p) REVERT: A 540 ASN cc_start: 0.7676 (m-40) cc_final: 0.6933 (t0) REVERT: A 645 THR cc_start: 0.8900 (m) cc_final: 0.8584 (p) REVERT: A 663 ASP cc_start: 0.8618 (t0) cc_final: 0.8403 (t0) REVERT: A 765 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8267 (mtm-85) REVERT: A 904 TYR cc_start: 0.8100 (m-80) cc_final: 0.7661 (m-80) REVERT: A 979 ASP cc_start: 0.7960 (m-30) cc_final: 0.6792 (t0) REVERT: C 65 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: C 118 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6334 (mm) REVERT: C 170 TYR cc_start: 0.7393 (t80) cc_final: 0.6986 (m-80) REVERT: C 335 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6925 (pp) REVERT: C 388 ASN cc_start: 0.7210 (p0) cc_final: 0.6766 (p0) REVERT: C 396 TYR cc_start: 0.6868 (m-80) cc_final: 0.6279 (m-80) REVERT: C 540 ASN cc_start: 0.7679 (m110) cc_final: 0.7131 (t0) REVERT: C 747 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7564 (m) REVERT: C 751 ASN cc_start: 0.8662 (m-40) cc_final: 0.8261 (m110) REVERT: C 752 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 820 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8538 (m-30) REVERT: C 979 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7641 (t70) REVERT: C 994 ASP cc_start: 0.8775 (t70) cc_final: 0.8456 (t0) REVERT: C 1144 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7819 (mm-30) outliers start: 152 outliers final: 88 residues processed: 338 average time/residue: 0.1407 time to fit residues: 81.5964 Evaluate side-chains 273 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 171 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain B residue 271 GLN 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 396 TYR 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 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 692 ILE Chi-restraints excluded: chain B residue 705 VAL 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 1081 ILE 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 207 HIS 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 284 THR 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 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 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 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 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 213 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 335 LEU 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 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 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 912 THR 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 1144 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 109 optimal weight: 6.9990 chunk 129 optimal weight: 0.0370 chunk 215 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 49 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A1010 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.183300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125105 restraints weight = 39369.656| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.73 r_work: 0.3377 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26790 Z= 0.125 Angle : 0.662 13.888 36587 Z= 0.330 Chirality : 0.048 0.382 4246 Planarity : 0.006 0.136 4655 Dihedral : 5.071 40.333 3492 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.51 % Favored : 92.31 % Rotamer: Outliers : 3.17 % Allowed : 25.19 % Favored : 71.64 % 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: -1.85 (0.14), residues: 3237 helix: 1.18 (0.21), residues: 675 sheet: -0.75 (0.19), residues: 636 loop : -2.44 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 319 TYR 0.018 0.001 TYR A 170 PHE 0.019 0.001 PHE C 338 TRP 0.019 0.001 TRP A 633 HIS 0.018 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (26710) covalent geometry : angle 0.63930 / 0.32 (36380) SS BOND : bond 0.00472 / 0.28 ( 33) SS BOND : angle 1.66570 / 1.14 ( 66) hydrogen bonds : bond 0.04217 / 2.73 ( 803) hydrogen bonds : angle 5.51627 / 3.80 ( 2313) link_BETA1-4 : bond 0.00455 / 0.31 ( 12) link_BETA1-4 : angle 1.38021 / 0.91 ( 36) link_NAG-ASN : bond 0.00663 / 0.44 ( 35) link_NAG-ASN : angle 2.97902 / 2.14 ( 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 286 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 GLN cc_start: 0.5085 (OUTLIER) cc_final: 0.4682 (mm-40) REVERT: B 697 MET cc_start: 0.8453 (mtp) cc_final: 0.8119 (mtp) REVERT: A 529 LYS cc_start: 0.7347 (mmmt) cc_final: 0.6884 (pttm) REVERT: A 540 ASN cc_start: 0.7596 (m-40) cc_final: 0.7236 (t0) REVERT: A 645 THR cc_start: 0.8885 (m) cc_final: 0.8592 (p) REVERT: A 663 ASP cc_start: 0.8657 (t0) cc_final: 0.8454 (t0) REVERT: A 751 ASN cc_start: 0.8574 (m110) cc_final: 0.8312 (m-40) REVERT: C 170 TYR cc_start: 0.7315 (t80) cc_final: 0.6789 (m-80) REVERT: C 335 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6840 (pp) REVERT: C 356 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7056 (mmtm) REVERT: C 388 ASN cc_start: 0.7114 (p0) cc_final: 0.6654 (p0) REVERT: C 540 ASN cc_start: 0.7559 (m110) cc_final: 0.6984 (t0) REVERT: C 596 SER cc_start: 0.9279 (t) cc_final: 0.8826 (m) REVERT: C 645 THR cc_start: 0.8756 (m) cc_final: 0.8489 (p) REVERT: C 747 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7535 (m) REVERT: C 751 ASN cc_start: 0.8634 (m-40) cc_final: 0.8206 (m110) REVERT: C 979 ASP cc_start: 0.8136 (m-30) cc_final: 0.7592 (t70) REVERT: C 994 ASP cc_start: 0.8727 (t70) cc_final: 0.8415 (t0) outliers start: 90 outliers final: 68 residues processed: 277 average time/residue: 0.1330 time to fit residues: 63.7755 Evaluate side-chains 250 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 179 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain B residue 271 GLN 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 552 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 791 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 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER 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 284 THR 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 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 620 VAL 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 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 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 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 335 LEU 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 439 ASN 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 791 THR 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=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: 20.0000 chunk 291 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 254 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 299 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 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 = 0.4342 r_free = 0.4342 target = 0.183459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124942 restraints weight = 39684.834| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.90 r_work: 0.3374 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26790 Z= 0.131 Angle : 0.652 11.193 36587 Z= 0.323 Chirality : 0.047 0.301 4246 Planarity : 0.006 0.137 4655 Dihedral : 4.852 41.736 3492 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 3.25 % Allowed : 24.87 % Favored : 71.89 % 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: 1.39 (0.21), residues: 669 sheet: -0.63 (0.19), residues: 639 loop : -2.42 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.016 0.001 TYR A 904 PHE 0.020 0.001 PHE C 392 TRP 0.014 0.001 TRP A 633 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (26710) covalent geometry : angle 0.63233 / 0.32 (36380) SS BOND : bond 0.00478 / 0.27 ( 33) SS BOND : angle 1.81204 / 1.34 ( 66) hydrogen bonds : bond 0.04012 / 2.60 ( 803) hydrogen bonds : angle 5.30075 / 3.63 ( 2313) link_BETA1-4 : bond 0.00468 / 0.34 ( 12) link_BETA1-4 : angle 1.34849 / 0.89 ( 36) link_NAG-ASN : bond 0.00568 / 0.37 ( 35) link_NAG-ASN : angle 2.61732 / 1.91 ( 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 281 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 189 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 GLN cc_start: 0.5296 (OUTLIER) cc_final: 0.4830 (mm-40) REVERT: B 697 MET cc_start: 0.8465 (mtp) cc_final: 0.8054 (mtp) REVERT: A 387 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6203 (mp) REVERT: A 529 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6925 (pttm) REVERT: A 540 ASN cc_start: 0.7584 (m-40) cc_final: 0.6919 (t0) REVERT: A 637 SER cc_start: 0.3506 (OUTLIER) cc_final: 0.3020 (p) REVERT: A 645 THR cc_start: 0.8863 (m) cc_final: 0.8473 (p) REVERT: A 751 ASN cc_start: 0.8461 (m110) cc_final: 0.8174 (m-40) REVERT: C 170 TYR cc_start: 0.7387 (t80) cc_final: 0.6784 (m-80) REVERT: C 335 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6827 (pp) REVERT: C 356 LYS cc_start: 0.7386 (mmtt) cc_final: 0.6939 (mmtm) REVERT: C 368 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5290 (mp) REVERT: C 388 ASN cc_start: 0.7191 (p0) cc_final: 0.6720 (p0) REVERT: C 540 ASN cc_start: 0.7469 (m110) cc_final: 0.6823 (t0) REVERT: C 564 GLN cc_start: 0.7098 (mm110) cc_final: 0.6769 (mt0) REVERT: C 596 SER cc_start: 0.9344 (t) cc_final: 0.8874 (m) REVERT: C 747 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7416 (m) REVERT: C 751 ASN cc_start: 0.8576 (m-40) cc_final: 0.8130 (m110) REVERT: C 979 ASP cc_start: 0.8141 (m-30) cc_final: 0.7531 (t70) outliers start: 92 outliers final: 75 residues processed: 270 average time/residue: 0.1268 time to fit residues: 58.8148 Evaluate side-chains 257 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 176 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 GLN 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 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 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 1002 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 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 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 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 740 MET Chi-restraints excluded: chain A residue 761 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 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 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL 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 335 LEU Chi-restraints excluded: chain C residue 368 LEU 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 439 ASN 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 912 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: 7.9990 chunk 238 optimal weight: 0.1980 chunk 243 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4331 r_free = 0.4331 target = 0.182479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120028 restraints weight = 39613.878| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.62 r_work: 0.3397 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26790 Z= 0.152 Angle : 0.655 14.917 36587 Z= 0.324 Chirality : 0.048 0.303 4246 Planarity : 0.006 0.140 4655 Dihedral : 4.809 41.617 3492 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.59 % Favored : 91.20 % Rotamer: Outliers : 3.32 % Allowed : 24.73 % Favored : 71.96 % 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: -1.71 (0.14), residues: 3237 helix: 1.36 (0.21), residues: 681 sheet: -0.67 (0.18), residues: 699 loop : -2.42 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.016 0.001 TYR A 904 PHE 0.020 0.001 PHE C 562 TRP 0.013 0.001 TRP A 633 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (26710) covalent geometry : angle 0.63552 / 0.32 (36380) SS BOND : bond 0.00394 / 0.23 ( 33) SS BOND : angle 1.86926 / 1.35 ( 66) hydrogen bonds : bond 0.04115 / 2.66 ( 803) hydrogen bonds : angle 5.24617 / 3.60 ( 2313) link_BETA1-4 : bond 0.00431 / 0.30 ( 12) link_BETA1-4 : angle 1.36463 / 0.91 ( 36) link_NAG-ASN : bond 0.00568 / 0.36 ( 35) link_NAG-ASN : angle 2.56873 / 1.88 ( 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 279 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 185 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 GLN cc_start: 0.5578 (OUTLIER) cc_final: 0.5143 (mm-40) REVERT: B 697 MET cc_start: 0.8379 (mtp) cc_final: 0.7979 (mtp) REVERT: A 329 PHE cc_start: 0.6294 (m-10) cc_final: 0.5894 (m-10) REVERT: A 387 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6135 (mp) REVERT: A 529 LYS cc_start: 0.7405 (mmmt) cc_final: 0.6961 (pttm) REVERT: A 540 ASN cc_start: 0.7701 (m-40) cc_final: 0.7026 (t0) REVERT: A 637 SER cc_start: 0.3863 (OUTLIER) cc_final: 0.3233 (p) REVERT: A 751 ASN cc_start: 0.8447 (m110) cc_final: 0.8184 (m110) REVERT: C 170 TYR cc_start: 0.7483 (t80) cc_final: 0.6985 (m-80) REVERT: C 335 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6842 (pp) REVERT: C 356 LYS cc_start: 0.7478 (mmtt) cc_final: 0.7018 (mmtm) REVERT: C 388 ASN cc_start: 0.7082 (p0) cc_final: 0.6586 (p0) REVERT: C 540 ASN cc_start: 0.7666 (m110) cc_final: 0.7011 (t0) REVERT: C 564 GLN cc_start: 0.7203 (mm110) cc_final: 0.6933 (mt0) REVERT: C 747 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7390 (m) REVERT: C 751 ASN cc_start: 0.8580 (m-40) cc_final: 0.8171 (m110) REVERT: C 755 GLN cc_start: 0.8821 (tt0) cc_final: 0.8417 (tt0) outliers start: 94 outliers final: 78 residues processed: 264 average time/residue: 0.1218 time to fit residues: 55.6447 Evaluate side-chains 263 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 180 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 271 GLN 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 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 1002 GLN Chi-restraints excluded: chain A residue 49 HIS 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 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 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 387 LEU Chi-restraints excluded: chain A residue 402 ILE 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 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 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 740 MET Chi-restraints excluded: chain A residue 761 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 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 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE 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 335 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL 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 912 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 323 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 238 optimal weight: 0.0040 chunk 258 optimal weight: 0.9980 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.186033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124803 restraints weight = 39683.468| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.79 r_work: 0.3413 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26790 Z= 0.111 Angle : 0.631 14.957 36587 Z= 0.312 Chirality : 0.046 0.301 4246 Planarity : 0.006 0.141 4655 Dihedral : 4.627 41.221 3492 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.09 % Favored : 91.69 % Rotamer: Outliers : 2.93 % Allowed : 25.22 % Favored : 71.85 % 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: -1.57 (0.14), residues: 3237 helix: 1.44 (0.21), residues: 678 sheet: -0.49 (0.19), residues: 657 loop : -2.33 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.017 0.001 TYR B 396 PHE 0.019 0.001 PHE C 562 TRP 0.015 0.001 TRP A 633 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (26710) covalent geometry : angle 0.61510 / 0.31 (36380) SS BOND : bond 0.00339 / 0.21 ( 33) SS BOND : angle 1.52714 / 1.12 ( 66) hydrogen bonds : bond 0.03652 / 2.37 ( 803) hydrogen bonds : angle 5.09349 / 3.49 ( 2313) link_BETA1-4 : bond 0.00449 / 0.32 ( 12) link_BETA1-4 : angle 1.14315 / 0.76 ( 36) link_NAG-ASN : bond 0.00559 / 0.37 ( 35) link_NAG-ASN : angle 2.39404 / 1.76 ( 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 270 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 187 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 GLN cc_start: 0.5584 (OUTLIER) cc_final: 0.5095 (mm-40) REVERT: A 102 ARG cc_start: 0.6451 (mpt-90) cc_final: 0.6216 (mpt-90) REVERT: A 529 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6779 (pttm) REVERT: A 540 ASN cc_start: 0.7669 (m-40) cc_final: 0.6989 (t0) REVERT: A 637 SER cc_start: 0.3691 (OUTLIER) cc_final: 0.3075 (p) REVERT: A 645 THR cc_start: 0.8760 (m) cc_final: 0.8420 (p) REVERT: A 751 ASN cc_start: 0.8446 (m110) cc_final: 0.8203 (m-40) REVERT: A 904 TYR cc_start: 0.7743 (m-80) cc_final: 0.7090 (m-80) REVERT: C 170 TYR cc_start: 0.7429 (t80) cc_final: 0.6960 (m-80) REVERT: C 335 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6825 (pp) REVERT: C 356 LYS cc_start: 0.7483 (mmtt) cc_final: 0.7009 (mmtm) REVERT: C 368 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5257 (mp) REVERT: C 388 ASN cc_start: 0.7159 (p0) cc_final: 0.6660 (p0) REVERT: C 540 ASN cc_start: 0.7596 (m110) cc_final: 0.6936 (t0) REVERT: C 564 GLN cc_start: 0.7140 (mm110) cc_final: 0.6924 (mt0) REVERT: C 747 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7474 (m) REVERT: C 751 ASN cc_start: 0.8567 (m-40) cc_final: 0.8150 (m110) REVERT: C 755 GLN cc_start: 0.8811 (tt0) cc_final: 0.8381 (tt0) outliers start: 83 outliers final: 73 residues processed: 256 average time/residue: 0.1327 time to fit residues: 58.6503 Evaluate side-chains 259 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU 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 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 1002 GLN Chi-restraints excluded: chain A residue 49 HIS 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 293 LEU Chi-restraints excluded: chain A residue 303 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 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 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 761 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 1005 GLN Chi-restraints excluded: chain A residue 1122 VAL 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 140 PHE 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 335 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 439 ASN 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 791 THR Chi-restraints excluded: chain C residue 912 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 296 optimal weight: 3.9990 chunk 316 optimal weight: 0.3980 chunk 263 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 0.0270 chunk 134 optimal weight: 0.5980 chunk 292 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 21 optimal weight: 0.0170 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1002 GLN A1119 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.185290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124467 restraints weight = 39571.814| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.71 r_work: 0.3420 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26790 Z= 0.113 Angle : 0.623 17.051 36587 Z= 0.307 Chirality : 0.046 0.303 4246 Planarity : 0.006 0.141 4655 Dihedral : 4.548 40.907 3492 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.09 % Favored : 91.66 % Rotamer: Outliers : 3.07 % Allowed : 25.08 % Favored : 71.85 % 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: -1.51 (0.14), residues: 3237 helix: 1.35 (0.21), residues: 687 sheet: -0.43 (0.19), residues: 672 loop : -2.27 (0.13), residues: 1878 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 0.020 0.001 PHE B 192 TRP 0.014 0.001 TRP A 633 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (26710) covalent geometry : angle 0.60721 / 0.30 (36380) SS BOND : bond 0.00321 / 0.19 ( 33) SS BOND : angle 1.50642 / 1.10 ( 66) hydrogen bonds : bond 0.03601 / 2.33 ( 803) hydrogen bonds : angle 5.00045 / 3.43 ( 2313) link_BETA1-4 : bond 0.00411 / 0.29 ( 12) link_BETA1-4 : angle 1.15012 / 0.77 ( 36) link_NAG-ASN : bond 0.00549 / 0.36 ( 35) link_NAG-ASN : angle 2.32482 / 1.71 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8457.41 seconds wall clock time: 154 minutes 53.04 seconds (9293.04 seconds total)