Starting phenix.real_space_refine on Mon Jul 6 22:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o7p_12752/07_2026/7o7p_12752.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 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 172 5.16 5 C 25586 2.51 5 N 6717 2.21 5 O 7820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.06s 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: 40295 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 9967 Classifications: {'peptide': 1277} Link IDs: {'PTRANS': 66, 'TRANS': 1210} Chain breaks: 1 Chain: "B" Number of atoms: 9944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1275, 9944 Classifications: {'peptide': 1275} Link IDs: {'PTRANS': 66, 'TRANS': 1208} Chain breaks: 1 Chain: "C" Number of atoms: 9940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 9940 Classifications: {'peptide': 1274} Link IDs: {'PTRANS': 66, 'TRANS': 1207} Chain breaks: 1 Chain: "D" Number of atoms: 9940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 9940 Classifications: {'peptide': 1274} Link IDs: {'PTRANS': 66, 'TRANS': 1207} Chain breaks: 1 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.49, per 1000 atoms: 0.24 Number of scatterers: 40295 At special positions: 0 Unit cell: (214.635, 151.815, 158.097, 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 172 16.00 O 7820 8.00 N 6717 7.00 C 25586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.02 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.07 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.05 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.02 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.02 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.02 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.04 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.02 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.03 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.03 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.07 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.03 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.05 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 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-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 247 " " NAG D2004 " - " ASN D 396 " " NAG D2005 " - " ASN D 410 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 869 " " NAG L 1 " - " ASN D 991 " Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.8 seconds 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9558 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 removed outlier: 4.414A pdb=" N LEU A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 5.387A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 4.010A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.924A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 6.053A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 Proline residue: B 982 - end of helix removed outlier: 3.933A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 Processing helix chain 'B' and resid 1039 through 1055 Processing helix chain 'B' and resid 1060 through 1073 Processing helix chain 'B' and resid 1098 through 1111 Processing helix chain 'B' and resid 1119 through 1137 Processing helix chain 'B' and resid 1144 through 1157 Processing helix chain 'B' and resid 1160 through 1172 Processing helix chain 'B' and resid 1225 through 1241 Processing helix chain 'B' and resid 1251 through 1268 Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 removed outlier: 4.414A pdb=" N LEU C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 5.387A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 4.010A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 removed outlier: 3.924A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 Processing helix chain 'D' and resid 953 through 965 removed outlier: 6.053A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 Proline residue: D 982 - end of helix removed outlier: 3.933A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 Processing helix chain 'D' and resid 1039 through 1055 Processing helix chain 'D' and resid 1060 through 1073 Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 Processing helix chain 'D' and resid 1144 through 1157 Processing helix chain 'D' and resid 1160 through 1172 Processing helix chain 'D' and resid 1225 through 1241 Processing helix chain 'D' and resid 1251 through 1268 Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' 536 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6742 1.31 - 1.44: 10711 1.44 - 1.56: 23464 1.56 - 1.69: 10 1.69 - 1.82: 252 Bond restraints: 41179 Sorted by residual: bond pdb=" C7 NAG B2001 " pdb=" N2 NAG B2001 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C7 NAG D2001 " pdb=" N2 NAG D2001 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C7 NAG C2003 " pdb=" N2 NAG C2003 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C7 NAG A2003 " pdb=" N2 NAG A2003 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C7 NAG A2004 " pdb=" N2 NAG A2004 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 41174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 54684 3.27 - 6.54: 1188 6.54 - 9.81: 66 9.81 - 13.07: 8 13.07 - 16.34: 2 Bond angle restraints: 55948 Sorted by residual: angle pdb=" CA CYS B 821 " pdb=" C CYS B 821 " pdb=" N ILE B 822 " ideal model delta sigma weight residual 116.39 106.28 10.11 1.17e+00 7.31e-01 7.47e+01 angle pdb=" CA CYS D 821 " pdb=" C CYS D 821 " pdb=" N ILE D 822 " ideal model delta sigma weight residual 116.39 106.28 10.11 1.17e+00 7.31e-01 7.47e+01 angle pdb=" CA CYS D 821 " pdb=" CB CYS D 821 " pdb=" SG CYS D 821 " ideal model delta sigma weight residual 114.40 130.74 -16.34 2.30e+00 1.89e-01 5.05e+01 angle pdb=" CA CYS B 821 " pdb=" CB CYS B 821 " pdb=" SG CYS B 821 " ideal model delta sigma weight residual 114.40 130.74 -16.34 2.30e+00 1.89e-01 5.05e+01 angle pdb=" N ILE C1112 " pdb=" CA ILE C1112 " pdb=" C ILE C1112 " ideal model delta sigma weight residual 109.02 103.41 5.61 9.30e-01 1.16e+00 3.64e+01 ... (remaining 55943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21864 17.93 - 35.87: 2218 35.87 - 53.80: 409 53.80 - 71.73: 93 71.73 - 89.67: 32 Dihedral angle restraints: 24616 sinusoidal: 9770 harmonic: 14846 Sorted by residual: dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual 93.00 152.34 -59.34 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS C 431 " pdb=" SG CYS C 431 " pdb=" SG CYS D 278 " pdb=" CB CYS D 278 " ideal model delta sinusoidal sigma weight residual 93.00 152.34 -59.34 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS C 470 " pdb=" SG CYS C 470 " pdb=" SG CYS C 563 " pdb=" CB CYS C 563 " ideal model delta sinusoidal sigma weight residual 93.00 149.60 -56.60 1 1.00e+01 1.00e-02 4.32e+01 ... (remaining 24613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.793: 6470 0.793 - 1.586: 0 1.586 - 2.379: 0 2.379 - 3.173: 0 3.173 - 3.966: 1 Chirality restraints: 6471 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 991 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 1.57 -3.97 2.00e-01 2.50e+01 3.93e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.46e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-02 2.50e+03 2.25e+02 ... (remaining 6468 not shown) Planarity restraints: 7194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG I 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG H 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.058 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG K 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.134 2.00e-02 2.50e+03 ... (remaining 7191 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 528 2.51 - 3.10: 34727 3.10 - 3.70: 65138 3.70 - 4.30: 88768 4.30 - 4.90: 140952 Nonbonded interactions: 330113 Sorted by model distance: nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.908 3.040 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.908 3.040 nonbonded pdb=" OG1 THR B 656 " pdb=" O PRO C 657 " model vdw 2.017 3.040 nonbonded pdb=" O PRO A 657 " pdb=" OG1 THR D 656 " model vdw 2.017 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OG1 THR A 738 " model vdw 2.023 3.040 ... (remaining 330108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 1335 or resid 2001 through 2005)) selection = (chain 'B' and resid 28 through 2005) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 34.620 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 41259 Z= 0.486 Angle : 1.165 20.359 56144 Z= 0.644 Chirality : 0.075 3.966 6471 Planarity : 0.014 0.305 7166 Dihedral : 14.949 89.665 14926 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.65 % Favored : 87.04 % Rotamer: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.10), residues: 5084 helix: -1.90 (0.14), residues: 856 sheet: -2.58 (0.10), residues: 1802 loop : -3.81 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 360 TYR 0.026 0.003 TYR A 558 PHE 0.030 0.003 PHE B 735 TRP 0.028 0.003 TRP D 765 HIS 0.016 0.002 HIS D1182 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.49 (41179) covalent geometry : angle 1.14909 / 0.64 (55948) SS BOND : bond 0.01096 / 0.81 ( 44) SS BOND : angle 3.38132 / 2.35 ( 88) hydrogen bonds : bond 0.09646 / 6.46 ( 536) hydrogen bonds : angle 5.52873 / 3.78 ( 1608) link_BETA1-4 : bond 0.00252 / 0.13 ( 8) link_BETA1-4 : angle 1.76007 / 1.18 ( 24) link_NAG-ASN : bond 0.01346 / 0.80 ( 28) link_NAG-ASN : angle 3.83837 / 2.50 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1150 time to evaluate : 1.526 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9105 (ttt) cc_final: 0.8688 (ttm) REVERT: A 97 ASN cc_start: 0.8976 (t0) cc_final: 0.8689 (t0) REVERT: A 99 GLU cc_start: 0.9152 (tt0) cc_final: 0.8603 (mp0) REVERT: A 146 PHE cc_start: 0.9413 (p90) cc_final: 0.9071 (p90) REVERT: A 183 LEU cc_start: 0.8401 (mt) cc_final: 0.8190 (mt) REVERT: A 204 LYS cc_start: 0.6764 (mtpt) cc_final: 0.6508 (tppt) REVERT: A 209 LYS cc_start: 0.9418 (mtmt) cc_final: 0.8290 (mmtm) REVERT: A 229 PHE cc_start: 0.8951 (p90) cc_final: 0.8676 (p90) REVERT: A 270 ARG cc_start: 0.7569 (tpt-90) cc_final: 0.7008 (mtt90) REVERT: A 290 PHE cc_start: 0.9432 (m-80) cc_final: 0.9034 (m-80) REVERT: A 321 HIS cc_start: 0.8922 (m-70) cc_final: 0.8706 (m-70) REVERT: A 428 ARG cc_start: 0.5669 (mpt180) cc_final: 0.5029 (mtm180) REVERT: A 496 TYR cc_start: 0.7716 (m-80) cc_final: 0.7200 (m-80) REVERT: A 550 ASP cc_start: 0.8700 (m-30) cc_final: 0.8076 (m-30) REVERT: A 569 ASP cc_start: 0.8769 (m-30) cc_final: 0.8540 (m-30) REVERT: A 573 SER cc_start: 0.9158 (t) cc_final: 0.8929 (p) REVERT: A 650 ILE cc_start: 0.6290 (mm) cc_final: 0.5885 (mm) REVERT: A 669 PHE cc_start: 0.8455 (m-10) cc_final: 0.7982 (m-10) REVERT: A 670 LEU cc_start: 0.9592 (mp) cc_final: 0.9286 (pp) REVERT: A 688 MET cc_start: 0.8506 (ppp) cc_final: 0.8077 (ppp) REVERT: A 809 THR cc_start: 0.9337 (t) cc_final: 0.9009 (t) REVERT: A 870 PHE cc_start: 0.8554 (m-80) cc_final: 0.8328 (m-80) REVERT: A 933 LEU cc_start: 0.8932 (mt) cc_final: 0.8557 (mt) REVERT: A 965 LEU cc_start: 0.9156 (tt) cc_final: 0.8771 (tt) REVERT: A 975 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8399 (tp-100) REVERT: A 978 VAL cc_start: 0.8728 (t) cc_final: 0.8350 (t) REVERT: A 983 ASN cc_start: 0.9348 (m-40) cc_final: 0.9045 (m110) REVERT: A 988 ASP cc_start: 0.9094 (m-30) cc_final: 0.8799 (m-30) REVERT: A 1020 HIS cc_start: 0.8480 (m-70) cc_final: 0.7289 (m-70) REVERT: A 1028 PHE cc_start: 0.8454 (m-80) cc_final: 0.8184 (m-80) REVERT: A 1057 PHE cc_start: 0.8651 (t80) cc_final: 0.8359 (t80) REVERT: A 1076 ASP cc_start: 0.8506 (p0) cc_final: 0.7940 (m-30) REVERT: A 1154 PHE cc_start: 0.8566 (m-80) cc_final: 0.8051 (m-80) REVERT: A 1163 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8328 (mtp180) REVERT: A 1241 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8152 (mm110) REVERT: A 1312 TYR cc_start: 0.9527 (m-80) cc_final: 0.9018 (m-80) REVERT: B 32 MET cc_start: 0.9325 (ttt) cc_final: 0.8891 (ttp) REVERT: B 50 LEU cc_start: 0.9071 (tt) cc_final: 0.7740 (tt) REVERT: B 121 MET cc_start: 0.7761 (tpp) cc_final: 0.6968 (tpp) REVERT: B 146 PHE cc_start: 0.9250 (p90) cc_final: 0.8765 (p90) REVERT: B 222 GLU cc_start: 0.9429 (pt0) cc_final: 0.9185 (pm20) REVERT: B 316 TYR cc_start: 0.6131 (m-80) cc_final: 0.5554 (t80) REVERT: B 354 LYS cc_start: 0.8631 (tttp) cc_final: 0.7506 (mttt) REVERT: B 356 ASP cc_start: 0.8820 (m-30) cc_final: 0.8338 (p0) REVERT: B 406 GLN cc_start: 0.8929 (mp10) cc_final: 0.8715 (mp-120) REVERT: B 461 LEU cc_start: 0.9234 (mp) cc_final: 0.9026 (mm) REVERT: B 479 HIS cc_start: 0.8925 (m170) cc_final: 0.8502 (m170) REVERT: B 496 TYR cc_start: 0.7943 (m-80) cc_final: 0.7163 (m-80) REVERT: B 543 TYR cc_start: 0.8506 (p90) cc_final: 0.7480 (p90) REVERT: B 552 ILE cc_start: 0.8804 (pt) cc_final: 0.8534 (pt) REVERT: B 569 ASP cc_start: 0.9166 (t0) cc_final: 0.8761 (t70) REVERT: B 570 LEU cc_start: 0.9119 (tt) cc_final: 0.8419 (pt) REVERT: B 571 SER cc_start: 0.9163 (t) cc_final: 0.8474 (p) REVERT: B 572 PHE cc_start: 0.8072 (p90) cc_final: 0.7355 (p90) REVERT: B 635 ASN cc_start: 0.9118 (p0) cc_final: 0.8909 (p0) REVERT: B 638 ASP cc_start: 0.9121 (t70) cc_final: 0.8543 (p0) REVERT: B 666 MET cc_start: 0.7847 (tpp) cc_final: 0.7305 (ttm) REVERT: B 669 PHE cc_start: 0.8691 (m-80) cc_final: 0.8189 (m-80) REVERT: B 828 LEU cc_start: 0.8480 (pt) cc_final: 0.8270 (mm) REVERT: B 870 PHE cc_start: 0.9178 (t80) cc_final: 0.8772 (t80) REVERT: B 901 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8725 (mmtt) REVERT: B 935 LEU cc_start: 0.6858 (mt) cc_final: 0.6277 (mt) REVERT: B 985 TYR cc_start: 0.9029 (m-80) cc_final: 0.8641 (m-80) REVERT: B 1067 LEU cc_start: 0.7428 (tp) cc_final: 0.7146 (mt) REVERT: B 1089 ASN cc_start: 0.8244 (m-40) cc_final: 0.7848 (p0) REVERT: B 1224 THR cc_start: 0.8307 (p) cc_final: 0.7852 (t) REVERT: B 1227 ASP cc_start: 0.8531 (m-30) cc_final: 0.7736 (p0) REVERT: B 1237 TRP cc_start: 0.8534 (t60) cc_final: 0.7964 (t60) REVERT: B 1238 ILE cc_start: 0.7785 (mm) cc_final: 0.7248 (mm) REVERT: B 1331 ASN cc_start: 0.7073 (m110) cc_final: 0.6310 (t0) REVERT: C 32 MET cc_start: 0.9106 (ttt) cc_final: 0.8669 (ttm) REVERT: C 97 ASN cc_start: 0.8976 (t0) cc_final: 0.8689 (t0) REVERT: C 99 GLU cc_start: 0.9152 (tt0) cc_final: 0.8602 (mp0) REVERT: C 146 PHE cc_start: 0.9412 (p90) cc_final: 0.9071 (p90) REVERT: C 183 LEU cc_start: 0.8396 (mt) cc_final: 0.8186 (mt) REVERT: C 204 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6502 (tppt) REVERT: C 209 LYS cc_start: 0.9415 (mtmt) cc_final: 0.8290 (mmtm) REVERT: C 229 PHE cc_start: 0.8954 (p90) cc_final: 0.8679 (p90) REVERT: C 270 ARG cc_start: 0.7580 (tpt-90) cc_final: 0.7022 (mtt90) REVERT: C 290 PHE cc_start: 0.9428 (m-80) cc_final: 0.9030 (m-80) REVERT: C 321 HIS cc_start: 0.8925 (m-70) cc_final: 0.8708 (m-70) REVERT: C 428 ARG cc_start: 0.5671 (mpt180) cc_final: 0.5052 (mtm180) REVERT: C 496 TYR cc_start: 0.7718 (m-80) cc_final: 0.7193 (m-80) REVERT: C 550 ASP cc_start: 0.8685 (m-30) cc_final: 0.8089 (m-30) REVERT: C 569 ASP cc_start: 0.8767 (m-30) cc_final: 0.8537 (m-30) REVERT: C 573 SER cc_start: 0.9161 (t) cc_final: 0.8930 (p) REVERT: C 650 ILE cc_start: 0.6303 (mm) cc_final: 0.5892 (mm) REVERT: C 669 PHE cc_start: 0.8458 (m-10) cc_final: 0.7983 (m-10) REVERT: C 670 LEU cc_start: 0.9591 (mp) cc_final: 0.9285 (pp) REVERT: C 688 MET cc_start: 0.8509 (ppp) cc_final: 0.8078 (ppp) REVERT: C 809 THR cc_start: 0.9334 (t) cc_final: 0.9007 (t) REVERT: C 933 LEU cc_start: 0.8932 (mt) cc_final: 0.8558 (mt) REVERT: C 938 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8025 (p0) REVERT: C 965 LEU cc_start: 0.9157 (tt) cc_final: 0.8771 (tt) REVERT: C 975 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8402 (tp-100) REVERT: C 978 VAL cc_start: 0.8727 (t) cc_final: 0.8350 (t) REVERT: C 983 ASN cc_start: 0.9354 (m-40) cc_final: 0.9132 (m110) REVERT: C 1020 HIS cc_start: 0.8479 (m-70) cc_final: 0.7291 (m-70) REVERT: C 1028 PHE cc_start: 0.8456 (m-80) cc_final: 0.8187 (m-80) REVERT: C 1057 PHE cc_start: 0.8672 (t80) cc_final: 0.8377 (t80) REVERT: C 1076 ASP cc_start: 0.8503 (p0) cc_final: 0.7935 (m-30) REVERT: C 1150 LEU cc_start: 0.9431 (mm) cc_final: 0.9220 (mm) REVERT: C 1154 PHE cc_start: 0.8564 (m-80) cc_final: 0.8008 (m-80) REVERT: C 1163 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8326 (mtp180) REVERT: C 1241 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8152 (mm110) REVERT: C 1312 TYR cc_start: 0.9526 (m-80) cc_final: 0.9020 (m-80) REVERT: C 1335 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: D 32 MET cc_start: 0.9327 (ttt) cc_final: 0.8891 (ttp) REVERT: D 50 LEU cc_start: 0.9070 (tt) cc_final: 0.7738 (tt) REVERT: D 121 MET cc_start: 0.7759 (tpp) cc_final: 0.6985 (tpp) REVERT: D 146 PHE cc_start: 0.9249 (p90) cc_final: 0.8762 (p90) REVERT: D 222 GLU cc_start: 0.9430 (pt0) cc_final: 0.9187 (pm20) REVERT: D 316 TYR cc_start: 0.6135 (m-80) cc_final: 0.5560 (t80) REVERT: D 354 LYS cc_start: 0.8632 (tttp) cc_final: 0.7511 (mttt) REVERT: D 356 ASP cc_start: 0.8819 (m-30) cc_final: 0.8338 (p0) REVERT: D 406 GLN cc_start: 0.8929 (mp10) cc_final: 0.8715 (mp-120) REVERT: D 461 LEU cc_start: 0.9236 (mp) cc_final: 0.9029 (mm) REVERT: D 479 HIS cc_start: 0.8928 (m170) cc_final: 0.8506 (m170) REVERT: D 496 TYR cc_start: 0.7947 (m-80) cc_final: 0.7166 (m-80) REVERT: D 543 TYR cc_start: 0.8503 (p90) cc_final: 0.7482 (p90) REVERT: D 552 ILE cc_start: 0.8807 (pt) cc_final: 0.8540 (pt) REVERT: D 569 ASP cc_start: 0.9168 (t0) cc_final: 0.8762 (t70) REVERT: D 570 LEU cc_start: 0.9121 (tt) cc_final: 0.8419 (pt) REVERT: D 571 SER cc_start: 0.9162 (t) cc_final: 0.8471 (p) REVERT: D 572 PHE cc_start: 0.8074 (p90) cc_final: 0.7355 (p90) REVERT: D 635 ASN cc_start: 0.9122 (p0) cc_final: 0.8851 (p0) REVERT: D 666 MET cc_start: 0.7837 (tpp) cc_final: 0.7314 (ttm) REVERT: D 669 PHE cc_start: 0.8693 (m-80) cc_final: 0.8191 (m-80) REVERT: D 828 LEU cc_start: 0.8475 (pt) cc_final: 0.8267 (mm) REVERT: D 870 PHE cc_start: 0.9232 (t80) cc_final: 0.8806 (t80) REVERT: D 901 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8733 (mmtt) REVERT: D 935 LEU cc_start: 0.6859 (mt) cc_final: 0.6243 (mt) REVERT: D 985 TYR cc_start: 0.8992 (m-80) cc_final: 0.8608 (m-80) REVERT: D 1067 LEU cc_start: 0.7426 (tp) cc_final: 0.7142 (mt) REVERT: D 1089 ASN cc_start: 0.8246 (m-40) cc_final: 0.7847 (p0) REVERT: D 1224 THR cc_start: 0.8307 (p) cc_final: 0.7851 (t) REVERT: D 1227 ASP cc_start: 0.8528 (m-30) cc_final: 0.7734 (p0) REVERT: D 1237 TRP cc_start: 0.8535 (t60) cc_final: 0.7966 (t60) REVERT: D 1238 ILE cc_start: 0.7789 (mm) cc_final: 0.7252 (mm) REVERT: D 1331 ASN cc_start: 0.6770 (m110) cc_final: 0.6139 (t0) outliers start: 6 outliers final: 2 residues processed: 1156 average time/residue: 0.2606 time to fit residues: 486.2718 Evaluate side-chains 755 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 751 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 0.0170 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 9.9990 overall best weight: 3.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS A 691 GLN A 960 GLN A 976 ASN A1241 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 381 ASN B 424 ASN B 441 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS B 637 GLN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 GLN C 976 ASN C1241 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 381 ASN D 424 ASN D 441 HIS ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 HIS D 637 GLN ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN D1017 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.096384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074224 restraints weight = 168930.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.076976 restraints weight = 121913.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.079185 restraints weight = 93684.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080959 restraints weight = 74901.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082434 restraints weight = 61844.768| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 41259 Z= 0.224 Angle : 0.902 16.022 56144 Z= 0.448 Chirality : 0.053 0.466 6471 Planarity : 0.006 0.084 7166 Dihedral : 6.442 28.541 5444 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.58 % Favored : 89.34 % Rotamer: Outliers : 0.58 % Allowed : 6.78 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.11), residues: 5084 helix: -0.67 (0.16), residues: 862 sheet: -2.26 (0.11), residues: 1845 loop : -3.42 (0.11), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 370 TYR 0.023 0.002 TYR B1055 PHE 0.028 0.002 PHE D1154 TRP 0.034 0.002 TRP B1132 HIS 0.008 0.002 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (41179) covalent geometry : angle 0.88012 / 0.44 (55948) SS BOND : bond 0.00494 / 0.29 ( 44) SS BOND : angle 2.38714 / 1.50 ( 88) hydrogen bonds : bond 0.05372 / 3.58 ( 536) hydrogen bonds : angle 5.17970 / 3.54 ( 1608) link_BETA1-4 : bond 0.00907 / 0.44 ( 8) link_BETA1-4 : angle 2.81621 / 1.90 ( 24) link_NAG-ASN : bond 0.01207 / 0.81 ( 28) link_NAG-ASN : angle 4.39813 / 2.96 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 944 time to evaluate : 1.616 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9225 (ttt) cc_final: 0.8843 (ttm) REVERT: A 97 ASN cc_start: 0.9018 (t0) cc_final: 0.8736 (t0) REVERT: A 121 MET cc_start: 0.8444 (mmt) cc_final: 0.7990 (mpp) REVERT: A 132 GLN cc_start: 0.9393 (tt0) cc_final: 0.9179 (tm-30) REVERT: A 151 MET cc_start: 0.4804 (ttp) cc_final: 0.4505 (tpp) REVERT: A 209 LYS cc_start: 0.9424 (mtmt) cc_final: 0.8877 (ptpt) REVERT: A 270 ARG cc_start: 0.7611 (tpt-90) cc_final: 0.7351 (tpt170) REVERT: A 271 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8484 (mmtm) REVERT: A 290 PHE cc_start: 0.9460 (m-80) cc_final: 0.8995 (m-80) REVERT: A 389 ASN cc_start: 0.7786 (m-40) cc_final: 0.7417 (t0) REVERT: A 428 ARG cc_start: 0.5682 (mpt180) cc_final: 0.5081 (mtp85) REVERT: A 491 LYS cc_start: 0.9511 (mmpt) cc_final: 0.9288 (mmmt) REVERT: A 496 TYR cc_start: 0.7533 (m-80) cc_final: 0.7199 (m-80) REVERT: A 564 LEU cc_start: 0.8713 (tp) cc_final: 0.8048 (tt) REVERT: A 567 LYS cc_start: 0.9416 (mmpt) cc_final: 0.9137 (mmmt) REVERT: A 628 THR cc_start: 0.7549 (t) cc_final: 0.7057 (m) REVERT: A 666 MET cc_start: 0.8940 (ttm) cc_final: 0.8623 (ttm) REVERT: A 669 PHE cc_start: 0.8260 (m-10) cc_final: 0.8013 (m-10) REVERT: A 670 LEU cc_start: 0.9565 (mp) cc_final: 0.9260 (pp) REVERT: A 688 MET cc_start: 0.8783 (ppp) cc_final: 0.8479 (ppp) REVERT: A 800 TYR cc_start: 0.9029 (p90) cc_final: 0.8651 (p90) REVERT: A 870 PHE cc_start: 0.8470 (m-80) cc_final: 0.8166 (m-80) REVERT: A 975 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8479 (tp-100) REVERT: A 985 TYR cc_start: 0.8622 (m-80) cc_final: 0.8288 (m-10) REVERT: A 988 ASP cc_start: 0.9117 (m-30) cc_final: 0.8557 (m-30) REVERT: A 1028 PHE cc_start: 0.8459 (m-80) cc_final: 0.8243 (m-80) REVERT: A 1047 LYS cc_start: 0.9397 (ttmt) cc_final: 0.9176 (ptmm) REVERT: A 1057 PHE cc_start: 0.8675 (t80) cc_final: 0.8260 (t80) REVERT: A 1125 LEU cc_start: 0.9474 (mt) cc_final: 0.9240 (pp) REVERT: A 1128 LEU cc_start: 0.9334 (mt) cc_final: 0.9064 (mt) REVERT: A 1150 LEU cc_start: 0.9373 (mm) cc_final: 0.9063 (mm) REVERT: A 1154 PHE cc_start: 0.8457 (m-80) cc_final: 0.7043 (m-80) REVERT: A 1314 MET cc_start: 0.9181 (mpp) cc_final: 0.8930 (ptp) REVERT: A 1323 TYR cc_start: 0.7988 (t80) cc_final: 0.7661 (t80) REVERT: B 32 MET cc_start: 0.9117 (ttt) cc_final: 0.8653 (ttt) REVERT: B 50 LEU cc_start: 0.9058 (tt) cc_final: 0.8524 (tt) REVERT: B 121 MET cc_start: 0.7978 (tpp) cc_final: 0.6900 (tpp) REVERT: B 216 GLU cc_start: 0.8753 (pp20) cc_final: 0.8406 (pp20) REVERT: B 246 MET cc_start: 0.7181 (mtm) cc_final: 0.6595 (mtp) REVERT: B 310 GLN cc_start: 0.8514 (mp10) cc_final: 0.8124 (mp10) REVERT: B 354 LYS cc_start: 0.8652 (tttp) cc_final: 0.7606 (mttt) REVERT: B 356 ASP cc_start: 0.9110 (m-30) cc_final: 0.8479 (p0) REVERT: B 496 TYR cc_start: 0.7894 (m-80) cc_final: 0.7361 (m-80) REVERT: B 543 TYR cc_start: 0.8370 (p90) cc_final: 0.7563 (p90) REVERT: B 545 VAL cc_start: 0.9085 (t) cc_final: 0.8729 (m) REVERT: B 552 ILE cc_start: 0.8709 (pt) cc_final: 0.8392 (pt) REVERT: B 570 LEU cc_start: 0.9080 (tt) cc_final: 0.8831 (pt) REVERT: B 571 SER cc_start: 0.9188 (t) cc_final: 0.8948 (p) REVERT: B 635 ASN cc_start: 0.9159 (p0) cc_final: 0.8414 (p0) REVERT: B 669 PHE cc_start: 0.8654 (m-80) cc_final: 0.8385 (m-80) REVERT: B 734 TYR cc_start: 0.7988 (t80) cc_final: 0.7531 (t80) REVERT: B 858 TRP cc_start: 0.7709 (m-90) cc_final: 0.7173 (m-90) REVERT: B 870 PHE cc_start: 0.9221 (t80) cc_final: 0.8513 (t80) REVERT: B 901 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8641 (mmtt) REVERT: B 935 LEU cc_start: 0.7298 (mt) cc_final: 0.6832 (mt) REVERT: B 985 TYR cc_start: 0.9204 (m-80) cc_final: 0.8665 (m-80) REVERT: B 1067 LEU cc_start: 0.8075 (tp) cc_final: 0.7872 (mt) REVERT: B 1072 GLN cc_start: 0.9147 (mt0) cc_final: 0.8423 (tt0) REVERT: B 1224 THR cc_start: 0.8563 (p) cc_final: 0.7995 (t) REVERT: B 1227 ASP cc_start: 0.8663 (m-30) cc_final: 0.7785 (p0) REVERT: B 1323 TYR cc_start: 0.7559 (t80) cc_final: 0.7356 (t80) REVERT: B 1331 ASN cc_start: 0.6765 (m110) cc_final: 0.3714 (m110) REVERT: C 32 MET cc_start: 0.9231 (ttt) cc_final: 0.8859 (ttm) REVERT: C 97 ASN cc_start: 0.9041 (t0) cc_final: 0.8747 (t0) REVERT: C 121 MET cc_start: 0.8475 (mmt) cc_final: 0.8007 (mpp) REVERT: C 132 GLN cc_start: 0.9386 (tt0) cc_final: 0.9171 (tm-30) REVERT: C 151 MET cc_start: 0.4774 (ttp) cc_final: 0.4483 (tpp) REVERT: C 209 LYS cc_start: 0.9433 (mtmt) cc_final: 0.8880 (ptpt) REVERT: C 270 ARG cc_start: 0.7615 (tpt-90) cc_final: 0.7361 (tpt170) REVERT: C 271 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8493 (mmtm) REVERT: C 290 PHE cc_start: 0.9467 (m-80) cc_final: 0.9005 (m-80) REVERT: C 389 ASN cc_start: 0.7785 (m-40) cc_final: 0.7419 (t0) REVERT: C 428 ARG cc_start: 0.5699 (mpt180) cc_final: 0.5090 (mtp180) REVERT: C 491 LYS cc_start: 0.9516 (mmpt) cc_final: 0.9296 (mmmt) REVERT: C 496 TYR cc_start: 0.7536 (m-80) cc_final: 0.7192 (m-80) REVERT: C 564 LEU cc_start: 0.8702 (tp) cc_final: 0.8043 (tt) REVERT: C 567 LYS cc_start: 0.9429 (mmpt) cc_final: 0.9152 (mmmt) REVERT: C 627 LEU cc_start: 0.7811 (tp) cc_final: 0.7298 (tp) REVERT: C 666 MET cc_start: 0.8956 (ttm) cc_final: 0.8633 (ttm) REVERT: C 669 PHE cc_start: 0.8232 (m-10) cc_final: 0.7989 (m-10) REVERT: C 670 LEU cc_start: 0.9559 (mp) cc_final: 0.9256 (pp) REVERT: C 688 MET cc_start: 0.8753 (ppp) cc_final: 0.8460 (ppp) REVERT: C 800 TYR cc_start: 0.8988 (p90) cc_final: 0.8616 (p90) REVERT: C 975 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8493 (tp-100) REVERT: C 985 TYR cc_start: 0.8661 (m-80) cc_final: 0.8376 (m-10) REVERT: C 1028 PHE cc_start: 0.8466 (m-80) cc_final: 0.8253 (m-80) REVERT: C 1047 LYS cc_start: 0.9390 (ttmt) cc_final: 0.9173 (ptmm) REVERT: C 1057 PHE cc_start: 0.8676 (t80) cc_final: 0.8255 (t80) REVERT: C 1125 LEU cc_start: 0.9480 (mt) cc_final: 0.9234 (pp) REVERT: C 1128 LEU cc_start: 0.9348 (mt) cc_final: 0.9039 (mt) REVERT: C 1150 LEU cc_start: 0.9373 (mm) cc_final: 0.9052 (mm) REVERT: C 1154 PHE cc_start: 0.8514 (m-80) cc_final: 0.7082 (m-80) REVERT: C 1314 MET cc_start: 0.9170 (mpp) cc_final: 0.8924 (ptp) REVERT: C 1323 TYR cc_start: 0.7976 (t80) cc_final: 0.7644 (t80) REVERT: D 32 MET cc_start: 0.9127 (ttt) cc_final: 0.8667 (ttt) REVERT: D 50 LEU cc_start: 0.9052 (tt) cc_final: 0.8512 (tt) REVERT: D 121 MET cc_start: 0.8000 (tpp) cc_final: 0.6918 (tpp) REVERT: D 216 GLU cc_start: 0.8767 (pp20) cc_final: 0.8412 (pp20) REVERT: D 246 MET cc_start: 0.7179 (mtm) cc_final: 0.6597 (mtp) REVERT: D 310 GLN cc_start: 0.8496 (mp10) cc_final: 0.8112 (mp10) REVERT: D 354 LYS cc_start: 0.8660 (tttp) cc_final: 0.8001 (mtpp) REVERT: D 356 ASP cc_start: 0.9124 (m-30) cc_final: 0.8497 (p0) REVERT: D 493 LEU cc_start: 0.9040 (tp) cc_final: 0.8751 (tp) REVERT: D 496 TYR cc_start: 0.7892 (m-80) cc_final: 0.7366 (m-80) REVERT: D 543 TYR cc_start: 0.8393 (p90) cc_final: 0.7584 (p90) REVERT: D 545 VAL cc_start: 0.9104 (t) cc_final: 0.8561 (m) REVERT: D 552 ILE cc_start: 0.8710 (pt) cc_final: 0.8387 (pt) REVERT: D 570 LEU cc_start: 0.9077 (tt) cc_final: 0.8819 (pt) REVERT: D 571 SER cc_start: 0.9187 (t) cc_final: 0.8951 (p) REVERT: D 635 ASN cc_start: 0.9150 (p0) cc_final: 0.8438 (p0) REVERT: D 669 PHE cc_start: 0.8639 (m-80) cc_final: 0.8380 (m-80) REVERT: D 734 TYR cc_start: 0.7984 (t80) cc_final: 0.7540 (t80) REVERT: D 858 TRP cc_start: 0.7713 (m-90) cc_final: 0.7176 (m-90) REVERT: D 870 PHE cc_start: 0.9243 (t80) cc_final: 0.8564 (t80) REVERT: D 901 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8602 (mmtt) REVERT: D 935 LEU cc_start: 0.7332 (mt) cc_final: 0.6871 (mt) REVERT: D 985 TYR cc_start: 0.9212 (m-80) cc_final: 0.8682 (m-80) REVERT: D 1072 GLN cc_start: 0.9173 (mt0) cc_final: 0.8326 (tt0) REVERT: D 1224 THR cc_start: 0.8574 (p) cc_final: 0.8015 (t) REVERT: D 1227 ASP cc_start: 0.8668 (m-30) cc_final: 0.7793 (p0) REVERT: D 1323 TYR cc_start: 0.7564 (t80) cc_final: 0.7352 (t80) REVERT: D 1331 ASN cc_start: 0.6652 (m110) cc_final: 0.3835 (m110) outliers start: 26 outliers final: 4 residues processed: 954 average time/residue: 0.2483 time to fit residues: 390.5375 Evaluate side-chains 696 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 692 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 367 optimal weight: 0.0370 chunk 354 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 295 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 384 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 425 optimal weight: 2.9990 overall best weight: 3.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS A 976 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 327 GLN B 441 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS C 691 GLN C 976 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 327 GLN D 441 HIS ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.092955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.071137 restraints weight = 169413.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.073939 restraints weight = 118874.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.076160 restraints weight = 89788.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077905 restraints weight = 71127.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.079332 restraints weight = 58344.117| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 41259 Z= 0.214 Angle : 0.842 14.465 56144 Z= 0.420 Chirality : 0.051 0.360 6471 Planarity : 0.006 0.076 7166 Dihedral : 6.205 32.221 5444 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.76 % Favored : 89.16 % Rotamer: Outliers : 0.31 % Allowed : 6.09 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.11), residues: 5084 helix: -0.19 (0.16), residues: 870 sheet: -2.00 (0.11), residues: 1774 loop : -3.26 (0.11), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 787 TYR 0.024 0.002 TYR B 734 PHE 0.048 0.002 PHE D1049 TRP 0.025 0.003 TRP D 436 HIS 0.008 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (41179) covalent geometry : angle 0.82511 / 0.42 (55948) SS BOND : bond 0.00667 / 0.33 ( 44) SS BOND : angle 2.15524 / 1.33 ( 88) hydrogen bonds : bond 0.04998 / 3.36 ( 536) hydrogen bonds : angle 5.01431 / 3.44 ( 1608) link_BETA1-4 : bond 0.00517 / 0.27 ( 8) link_BETA1-4 : angle 2.36700 / 1.51 ( 24) link_NAG-ASN : bond 0.00916 / 0.57 ( 28) link_NAG-ASN : angle 3.71780 / 2.50 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 907 time to evaluate : 1.437 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9298 (ttt) cc_final: 0.8938 (ttm) REVERT: A 98 GLU cc_start: 0.8876 (pm20) cc_final: 0.8636 (pm20) REVERT: A 121 MET cc_start: 0.8633 (mmt) cc_final: 0.8341 (mpp) REVERT: A 183 LEU cc_start: 0.8265 (tp) cc_final: 0.7988 (tp) REVERT: A 209 LYS cc_start: 0.9487 (mtmt) cc_final: 0.8766 (mmtm) REVERT: A 229 PHE cc_start: 0.8686 (p90) cc_final: 0.8485 (p90) REVERT: A 251 CYS cc_start: 0.8320 (m) cc_final: 0.7864 (t) REVERT: A 290 PHE cc_start: 0.9466 (m-80) cc_final: 0.8946 (m-80) REVERT: A 428 ARG cc_start: 0.5682 (mpt180) cc_final: 0.5104 (mtm180) REVERT: A 464 MET cc_start: 0.9498 (tpt) cc_final: 0.9193 (ttm) REVERT: A 491 LYS cc_start: 0.9495 (mmpt) cc_final: 0.9252 (mmmt) REVERT: A 496 TYR cc_start: 0.7700 (m-80) cc_final: 0.7408 (m-80) REVERT: A 564 LEU cc_start: 0.8535 (tp) cc_final: 0.7654 (tt) REVERT: A 567 LYS cc_start: 0.9487 (mmpt) cc_final: 0.9231 (mmmt) REVERT: A 626 ASP cc_start: 0.8239 (p0) cc_final: 0.8039 (p0) REVERT: A 627 LEU cc_start: 0.8251 (mm) cc_final: 0.7619 (mt) REVERT: A 666 MET cc_start: 0.8980 (ttm) cc_final: 0.8382 (ptm) REVERT: A 669 PHE cc_start: 0.8257 (m-10) cc_final: 0.7970 (m-10) REVERT: A 670 LEU cc_start: 0.9568 (mp) cc_final: 0.9222 (pp) REVERT: A 800 TYR cc_start: 0.9048 (p90) cc_final: 0.8716 (p90) REVERT: A 870 PHE cc_start: 0.8515 (m-80) cc_final: 0.8284 (m-80) REVERT: A 933 LEU cc_start: 0.9270 (mt) cc_final: 0.9042 (mt) REVERT: A 975 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8514 (tp-100) REVERT: A 988 ASP cc_start: 0.9148 (m-30) cc_final: 0.8581 (m-30) REVERT: A 1028 PHE cc_start: 0.8544 (m-80) cc_final: 0.8326 (m-80) REVERT: A 1057 PHE cc_start: 0.8697 (t80) cc_final: 0.8346 (t80) REVERT: A 1128 LEU cc_start: 0.9405 (mt) cc_final: 0.9181 (mt) REVERT: A 1144 VAL cc_start: 0.8517 (p) cc_final: 0.8238 (m) REVERT: A 1150 LEU cc_start: 0.9447 (mm) cc_final: 0.9116 (mm) REVERT: A 1154 PHE cc_start: 0.8554 (m-80) cc_final: 0.7379 (m-80) REVERT: A 1165 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 1241 GLN cc_start: 0.8586 (mm110) cc_final: 0.8360 (mm-40) REVERT: A 1314 MET cc_start: 0.9228 (mpp) cc_final: 0.8956 (ptp) REVERT: A 1323 TYR cc_start: 0.7978 (t80) cc_final: 0.7658 (t80) REVERT: B 50 LEU cc_start: 0.9106 (tt) cc_final: 0.8609 (tt) REVERT: B 121 MET cc_start: 0.8265 (tpp) cc_final: 0.7355 (tpp) REVERT: B 151 MET cc_start: 0.6298 (mtt) cc_final: 0.5732 (ttp) REVERT: B 194 LEU cc_start: 0.8434 (mm) cc_final: 0.8066 (mm) REVERT: B 216 GLU cc_start: 0.8947 (pp20) cc_final: 0.8569 (pp20) REVERT: B 222 GLU cc_start: 0.8900 (pp20) cc_final: 0.8594 (pp20) REVERT: B 354 LYS cc_start: 0.8627 (tttp) cc_final: 0.7723 (mttt) REVERT: B 356 ASP cc_start: 0.9176 (m-30) cc_final: 0.8556 (p0) REVERT: B 360 ARG cc_start: 0.8428 (mpt180) cc_final: 0.8224 (mpt-90) REVERT: B 389 ASN cc_start: 0.8685 (m-40) cc_final: 0.8442 (m-40) REVERT: B 392 ASN cc_start: 0.9541 (p0) cc_final: 0.9332 (p0) REVERT: B 394 TYR cc_start: 0.8007 (t80) cc_final: 0.7726 (t80) REVERT: B 415 MET cc_start: 0.5985 (pmm) cc_final: 0.5148 (pmm) REVERT: B 418 SER cc_start: 0.8927 (t) cc_final: 0.8541 (p) REVERT: B 461 LEU cc_start: 0.9271 (mp) cc_final: 0.9014 (mm) REVERT: B 496 TYR cc_start: 0.8014 (m-80) cc_final: 0.7586 (m-80) REVERT: B 521 LYS cc_start: 0.8542 (mttt) cc_final: 0.8313 (mttt) REVERT: B 543 TYR cc_start: 0.8579 (p90) cc_final: 0.8265 (p90) REVERT: B 552 ILE cc_start: 0.9073 (pt) cc_final: 0.8582 (pt) REVERT: B 571 SER cc_start: 0.9243 (t) cc_final: 0.9033 (p) REVERT: B 572 PHE cc_start: 0.8445 (p90) cc_final: 0.8048 (p90) REVERT: B 586 ARG cc_start: 0.9129 (ttt90) cc_final: 0.8439 (tpt90) REVERT: B 635 ASN cc_start: 0.9141 (p0) cc_final: 0.8554 (p0) REVERT: B 796 LEU cc_start: 0.8619 (pp) cc_final: 0.8369 (pp) REVERT: B 858 TRP cc_start: 0.7633 (m-90) cc_final: 0.7241 (m-90) REVERT: B 870 PHE cc_start: 0.9303 (t80) cc_final: 0.8963 (t80) REVERT: B 877 LEU cc_start: 0.8995 (mt) cc_final: 0.8577 (tt) REVERT: B 901 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8598 (mmtt) REVERT: B 933 LEU cc_start: 0.9478 (mt) cc_final: 0.9274 (mt) REVERT: B 935 LEU cc_start: 0.7497 (mt) cc_final: 0.7252 (tp) REVERT: B 985 TYR cc_start: 0.9198 (m-80) cc_final: 0.8773 (m-80) REVERT: B 1072 GLN cc_start: 0.9198 (mt0) cc_final: 0.8445 (tt0) REVERT: B 1205 GLU cc_start: 0.8347 (pt0) cc_final: 0.8060 (tt0) REVERT: B 1223 PRO cc_start: 0.6197 (Cg_exo) cc_final: 0.5728 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8583 (p) cc_final: 0.8057 (t) REVERT: B 1227 ASP cc_start: 0.8957 (m-30) cc_final: 0.8581 (p0) REVERT: B 1241 GLN cc_start: 0.7833 (mp-120) cc_final: 0.7505 (mp-120) REVERT: B 1331 ASN cc_start: 0.6852 (m110) cc_final: 0.4371 (m110) REVERT: C 32 MET cc_start: 0.9321 (ttt) cc_final: 0.8896 (ttm) REVERT: C 98 GLU cc_start: 0.8858 (pm20) cc_final: 0.8620 (pm20) REVERT: C 121 MET cc_start: 0.8672 (mmt) cc_final: 0.8363 (mpp) REVERT: C 183 LEU cc_start: 0.8244 (tp) cc_final: 0.7967 (tp) REVERT: C 209 LYS cc_start: 0.9485 (mtmt) cc_final: 0.8762 (mmtm) REVERT: C 229 PHE cc_start: 0.8691 (p90) cc_final: 0.8487 (p90) REVERT: C 251 CYS cc_start: 0.8319 (m) cc_final: 0.7879 (t) REVERT: C 290 PHE cc_start: 0.9465 (m-80) cc_final: 0.8957 (m-80) REVERT: C 428 ARG cc_start: 0.5687 (mpt180) cc_final: 0.5104 (mtm180) REVERT: C 464 MET cc_start: 0.9488 (tpt) cc_final: 0.9183 (ttm) REVERT: C 491 LYS cc_start: 0.9502 (mmpt) cc_final: 0.9262 (mmmt) REVERT: C 496 TYR cc_start: 0.7709 (m-80) cc_final: 0.7410 (m-80) REVERT: C 564 LEU cc_start: 0.8535 (tp) cc_final: 0.7650 (tt) REVERT: C 567 LYS cc_start: 0.9494 (mmpt) cc_final: 0.9244 (mmmt) REVERT: C 666 MET cc_start: 0.8988 (ttm) cc_final: 0.8379 (ptm) REVERT: C 669 PHE cc_start: 0.8258 (m-10) cc_final: 0.7974 (m-10) REVERT: C 670 LEU cc_start: 0.9561 (mp) cc_final: 0.9215 (pp) REVERT: C 800 TYR cc_start: 0.8995 (p90) cc_final: 0.8706 (p90) REVERT: C 931 LEU cc_start: 0.9137 (tp) cc_final: 0.8926 (tp) REVERT: C 933 LEU cc_start: 0.9264 (mt) cc_final: 0.9034 (mt) REVERT: C 975 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8529 (tp-100) REVERT: C 1028 PHE cc_start: 0.8548 (m-80) cc_final: 0.8334 (m-80) REVERT: C 1057 PHE cc_start: 0.8836 (t80) cc_final: 0.8365 (t80) REVERT: C 1128 LEU cc_start: 0.9414 (mt) cc_final: 0.9157 (mt) REVERT: C 1144 VAL cc_start: 0.8517 (p) cc_final: 0.8239 (m) REVERT: C 1150 LEU cc_start: 0.9458 (mm) cc_final: 0.9125 (mm) REVERT: C 1154 PHE cc_start: 0.8604 (m-80) cc_final: 0.7441 (m-80) REVERT: C 1165 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 1241 GLN cc_start: 0.8588 (mm110) cc_final: 0.8361 (mm-40) REVERT: C 1271 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6961 (mtt90) REVERT: C 1314 MET cc_start: 0.9216 (mpp) cc_final: 0.8936 (ptp) REVERT: C 1323 TYR cc_start: 0.7979 (t80) cc_final: 0.7654 (t80) REVERT: D 50 LEU cc_start: 0.9087 (tt) cc_final: 0.8743 (tt) REVERT: D 121 MET cc_start: 0.8277 (tpp) cc_final: 0.7358 (tpp) REVERT: D 151 MET cc_start: 0.6312 (mtt) cc_final: 0.5754 (ttp) REVERT: D 194 LEU cc_start: 0.8468 (mm) cc_final: 0.8133 (mm) REVERT: D 216 GLU cc_start: 0.8961 (pp20) cc_final: 0.8579 (pp20) REVERT: D 222 GLU cc_start: 0.8873 (pp20) cc_final: 0.8558 (pp20) REVERT: D 354 LYS cc_start: 0.8635 (tttp) cc_final: 0.7731 (mttt) REVERT: D 356 ASP cc_start: 0.9191 (m-30) cc_final: 0.8577 (p0) REVERT: D 360 ARG cc_start: 0.8419 (mpt180) cc_final: 0.8210 (mpt-90) REVERT: D 389 ASN cc_start: 0.8708 (m-40) cc_final: 0.8476 (m-40) REVERT: D 392 ASN cc_start: 0.9536 (p0) cc_final: 0.9327 (p0) REVERT: D 394 TYR cc_start: 0.7928 (t80) cc_final: 0.7487 (t80) REVERT: D 415 MET cc_start: 0.5997 (pmm) cc_final: 0.5159 (pmm) REVERT: D 418 SER cc_start: 0.8945 (t) cc_final: 0.8561 (p) REVERT: D 461 LEU cc_start: 0.9276 (mp) cc_final: 0.9018 (mm) REVERT: D 496 TYR cc_start: 0.8026 (m-80) cc_final: 0.7437 (m-80) REVERT: D 521 LYS cc_start: 0.8538 (mttt) cc_final: 0.8315 (mttt) REVERT: D 552 ILE cc_start: 0.9068 (pt) cc_final: 0.8562 (pt) REVERT: D 572 PHE cc_start: 0.8437 (p90) cc_final: 0.8075 (p90) REVERT: D 586 ARG cc_start: 0.9129 (ttt90) cc_final: 0.8423 (tpt90) REVERT: D 635 ASN cc_start: 0.9154 (p0) cc_final: 0.8609 (p0) REVERT: D 796 LEU cc_start: 0.8619 (pp) cc_final: 0.8337 (pp) REVERT: D 858 TRP cc_start: 0.7671 (m-90) cc_final: 0.7280 (m-90) REVERT: D 870 PHE cc_start: 0.9333 (t80) cc_final: 0.8946 (t80) REVERT: D 877 LEU cc_start: 0.9001 (mt) cc_final: 0.8585 (tt) REVERT: D 901 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8621 (mmtt) REVERT: D 935 LEU cc_start: 0.7490 (mt) cc_final: 0.7191 (tp) REVERT: D 985 TYR cc_start: 0.9236 (m-80) cc_final: 0.8765 (m-80) REVERT: D 1072 GLN cc_start: 0.9187 (mt0) cc_final: 0.8504 (tt0) REVERT: D 1205 GLU cc_start: 0.8346 (pt0) cc_final: 0.8067 (tt0) REVERT: D 1223 PRO cc_start: 0.6147 (Cg_exo) cc_final: 0.5654 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8567 (p) cc_final: 0.8033 (t) REVERT: D 1227 ASP cc_start: 0.8961 (m-30) cc_final: 0.8577 (p0) REVERT: D 1241 GLN cc_start: 0.7851 (mp-120) cc_final: 0.7520 (mp-120) REVERT: D 1328 LEU cc_start: 0.9522 (tp) cc_final: 0.9166 (tp) REVERT: D 1331 ASN cc_start: 0.6610 (m110) cc_final: 0.4198 (m110) outliers start: 14 outliers final: 4 residues processed: 915 average time/residue: 0.2450 time to fit residues: 370.3202 Evaluate side-chains 690 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 686 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 11 optimal weight: 8.9990 chunk 230 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 428 optimal weight: 0.4980 chunk 239 optimal weight: 0.7980 chunk 285 optimal weight: 20.0000 chunk 460 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 321 HIS ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 582 HIS A 647 ASN A 976 ASN A1051 GLN B 263 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN C 321 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS C 582 HIS C 647 ASN C 976 ASN D 263 HIS D 327 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.093670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.071995 restraints weight = 164895.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074718 restraints weight = 117428.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.076872 restraints weight = 89427.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.078577 restraints weight = 71288.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079943 restraints weight = 58727.931| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41259 Z= 0.156 Angle : 0.778 13.729 56144 Z= 0.386 Chirality : 0.050 0.395 6471 Planarity : 0.005 0.066 7166 Dihedral : 5.881 34.196 5444 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.52 % Favored : 90.40 % Rotamer: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.11), residues: 5084 helix: 0.02 (0.17), residues: 867 sheet: -1.65 (0.12), residues: 1714 loop : -3.13 (0.11), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 787 TYR 0.025 0.002 TYR B 256 PHE 0.043 0.002 PHE B1049 TRP 0.034 0.003 TRP B 436 HIS 0.006 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (41179) covalent geometry : angle 0.76271 / 0.38 (55948) SS BOND : bond 0.00746 / 0.43 ( 44) SS BOND : angle 2.00216 / 1.28 ( 88) hydrogen bonds : bond 0.04830 / 3.24 ( 536) hydrogen bonds : angle 4.71278 / 3.23 ( 1608) link_BETA1-4 : bond 0.00697 / 0.38 ( 8) link_BETA1-4 : angle 2.17227 / 1.36 ( 24) link_NAG-ASN : bond 0.00811 / 0.53 ( 28) link_NAG-ASN : angle 3.46560 / 2.35 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 888 time to evaluate : 1.622 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9316 (ttt) cc_final: 0.8850 (ttm) REVERT: A 98 GLU cc_start: 0.8889 (pm20) cc_final: 0.8620 (pm20) REVERT: A 121 MET cc_start: 0.8742 (mmt) cc_final: 0.8379 (mpp) REVERT: A 151 MET cc_start: 0.3471 (ttm) cc_final: 0.3008 (tpp) REVERT: A 209 LYS cc_start: 0.9485 (mtmt) cc_final: 0.8585 (mmtm) REVERT: A 251 CYS cc_start: 0.8252 (m) cc_final: 0.7944 (t) REVERT: A 271 LYS cc_start: 0.7480 (mptt) cc_final: 0.6853 (mptt) REVERT: A 289 LYS cc_start: 0.9457 (mppt) cc_final: 0.9247 (mmmt) REVERT: A 290 PHE cc_start: 0.9486 (m-80) cc_final: 0.9034 (m-80) REVERT: A 428 ARG cc_start: 0.5540 (mpt180) cc_final: 0.5002 (mtp180) REVERT: A 464 MET cc_start: 0.9450 (tpt) cc_final: 0.9182 (ttm) REVERT: A 491 LYS cc_start: 0.9472 (mmpt) cc_final: 0.9226 (mmmt) REVERT: A 496 TYR cc_start: 0.7798 (m-80) cc_final: 0.7470 (m-80) REVERT: A 567 LYS cc_start: 0.9533 (mmpt) cc_final: 0.9286 (mmmt) REVERT: A 627 LEU cc_start: 0.8667 (mm) cc_final: 0.8332 (mp) REVERT: A 666 MET cc_start: 0.9023 (ttm) cc_final: 0.8164 (ptp) REVERT: A 669 PHE cc_start: 0.8247 (m-10) cc_final: 0.8035 (m-10) REVERT: A 800 TYR cc_start: 0.9010 (p90) cc_final: 0.8792 (p90) REVERT: A 870 PHE cc_start: 0.8489 (m-80) cc_final: 0.8160 (m-80) REVERT: A 931 LEU cc_start: 0.9101 (tp) cc_final: 0.8875 (tp) REVERT: A 933 LEU cc_start: 0.9283 (mt) cc_final: 0.9039 (mt) REVERT: A 975 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8507 (tp-100) REVERT: A 983 ASN cc_start: 0.9357 (m-40) cc_final: 0.8909 (m110) REVERT: A 988 ASP cc_start: 0.8755 (m-30) cc_final: 0.8301 (m-30) REVERT: A 1057 PHE cc_start: 0.8847 (t80) cc_final: 0.8375 (t80) REVERT: A 1132 TRP cc_start: 0.8689 (t60) cc_final: 0.7807 (t60) REVERT: A 1133 LYS cc_start: 0.9420 (ttmt) cc_final: 0.9168 (tppt) REVERT: A 1144 VAL cc_start: 0.8477 (p) cc_final: 0.8147 (m) REVERT: A 1150 LEU cc_start: 0.9410 (mm) cc_final: 0.9129 (mm) REVERT: A 1154 PHE cc_start: 0.8855 (m-80) cc_final: 0.7772 (m-80) REVERT: A 1314 MET cc_start: 0.9218 (mpp) cc_final: 0.8984 (ptp) REVERT: B 50 LEU cc_start: 0.9121 (tt) cc_final: 0.8786 (tt) REVERT: B 121 MET cc_start: 0.8369 (tpp) cc_final: 0.7536 (tpp) REVERT: B 151 MET cc_start: 0.6358 (mtt) cc_final: 0.6116 (ttp) REVERT: B 216 GLU cc_start: 0.8990 (pp20) cc_final: 0.8588 (pp20) REVERT: B 290 PHE cc_start: 0.8916 (m-80) cc_final: 0.8711 (m-80) REVERT: B 310 GLN cc_start: 0.8721 (mp10) cc_final: 0.8486 (mp10) REVERT: B 354 LYS cc_start: 0.8511 (tttp) cc_final: 0.7695 (mttt) REVERT: B 356 ASP cc_start: 0.9188 (m-30) cc_final: 0.8811 (t0) REVERT: B 360 ARG cc_start: 0.8421 (mpt180) cc_final: 0.8122 (mpt-90) REVERT: B 389 ASN cc_start: 0.8566 (m-40) cc_final: 0.8266 (m-40) REVERT: B 415 MET cc_start: 0.6259 (pmm) cc_final: 0.5062 (pmm) REVERT: B 418 SER cc_start: 0.8908 (t) cc_final: 0.8389 (p) REVERT: B 479 HIS cc_start: 0.9303 (m90) cc_final: 0.9101 (m90) REVERT: B 496 TYR cc_start: 0.7997 (m-80) cc_final: 0.7549 (m-80) REVERT: B 539 ARG cc_start: 0.7655 (ttm170) cc_final: 0.6996 (ttm170) REVERT: B 543 TYR cc_start: 0.8737 (p90) cc_final: 0.8171 (p90) REVERT: B 545 VAL cc_start: 0.8937 (t) cc_final: 0.8186 (t) REVERT: B 552 ILE cc_start: 0.9120 (pt) cc_final: 0.8611 (pt) REVERT: B 571 SER cc_start: 0.9166 (t) cc_final: 0.8896 (p) REVERT: B 572 PHE cc_start: 0.8458 (p90) cc_final: 0.8077 (p90) REVERT: B 796 LEU cc_start: 0.8598 (pp) cc_final: 0.7956 (pp) REVERT: B 858 TRP cc_start: 0.7673 (m-90) cc_final: 0.7267 (m-90) REVERT: B 877 LEU cc_start: 0.8926 (mt) cc_final: 0.8507 (tt) REVERT: B 901 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8442 (mmtt) REVERT: B 935 LEU cc_start: 0.7627 (mt) cc_final: 0.7091 (tp) REVERT: B 965 LEU cc_start: 0.9128 (mt) cc_final: 0.8690 (mt) REVERT: B 985 TYR cc_start: 0.9153 (m-80) cc_final: 0.8694 (m-80) REVERT: B 1205 GLU cc_start: 0.8299 (pt0) cc_final: 0.7976 (tt0) REVERT: B 1223 PRO cc_start: 0.6095 (Cg_exo) cc_final: 0.5632 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8457 (p) cc_final: 0.7989 (t) REVERT: B 1227 ASP cc_start: 0.9102 (m-30) cc_final: 0.8863 (p0) REVERT: B 1241 GLN cc_start: 0.7732 (mp-120) cc_final: 0.7371 (mp10) REVERT: B 1328 LEU cc_start: 0.9512 (tp) cc_final: 0.9040 (tp) REVERT: B 1330 TYR cc_start: 0.8898 (p90) cc_final: 0.8680 (p90) REVERT: B 1331 ASN cc_start: 0.6682 (m110) cc_final: 0.4541 (m110) REVERT: C 32 MET cc_start: 0.9323 (ttt) cc_final: 0.8872 (ttm) REVERT: C 98 GLU cc_start: 0.8883 (pm20) cc_final: 0.8622 (pm20) REVERT: C 121 MET cc_start: 0.8778 (mmt) cc_final: 0.8405 (mpp) REVERT: C 151 MET cc_start: 0.3477 (ttm) cc_final: 0.3014 (tpp) REVERT: C 209 LYS cc_start: 0.9480 (mtmt) cc_final: 0.8583 (mmtm) REVERT: C 251 CYS cc_start: 0.8318 (m) cc_final: 0.7948 (t) REVERT: C 289 LYS cc_start: 0.9461 (mppt) cc_final: 0.9251 (mmmt) REVERT: C 290 PHE cc_start: 0.9487 (m-80) cc_final: 0.9039 (m-80) REVERT: C 301 TYR cc_start: 0.6722 (t80) cc_final: 0.6292 (t80) REVERT: C 428 ARG cc_start: 0.5528 (mpt180) cc_final: 0.4930 (mtm180) REVERT: C 464 MET cc_start: 0.9451 (tpt) cc_final: 0.9176 (ttm) REVERT: C 491 LYS cc_start: 0.9478 (mmpt) cc_final: 0.9232 (mmmt) REVERT: C 496 TYR cc_start: 0.7808 (m-80) cc_final: 0.7471 (m-80) REVERT: C 567 LYS cc_start: 0.9533 (mmpt) cc_final: 0.9288 (mmmt) REVERT: C 627 LEU cc_start: 0.8936 (mt) cc_final: 0.8723 (mt) REVERT: C 666 MET cc_start: 0.9041 (ttm) cc_final: 0.8223 (ptp) REVERT: C 669 PHE cc_start: 0.8242 (m-10) cc_final: 0.8020 (m-10) REVERT: C 670 LEU cc_start: 0.9531 (mp) cc_final: 0.9175 (pp) REVERT: C 798 MET cc_start: 0.8552 (ppp) cc_final: 0.8179 (ppp) REVERT: C 800 TYR cc_start: 0.8883 (p90) cc_final: 0.8640 (p90) REVERT: C 975 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8514 (tp-100) REVERT: C 988 ASP cc_start: 0.9149 (m-30) cc_final: 0.8879 (m-30) REVERT: C 1057 PHE cc_start: 0.8849 (t80) cc_final: 0.8378 (t80) REVERT: C 1132 TRP cc_start: 0.8702 (t60) cc_final: 0.7848 (t60) REVERT: C 1133 LYS cc_start: 0.9411 (ttmt) cc_final: 0.9165 (tppt) REVERT: C 1144 VAL cc_start: 0.8503 (p) cc_final: 0.8159 (m) REVERT: C 1150 LEU cc_start: 0.9411 (mm) cc_final: 0.9121 (mm) REVERT: C 1154 PHE cc_start: 0.8887 (m-80) cc_final: 0.7838 (m-80) REVERT: C 1314 MET cc_start: 0.9202 (mpp) cc_final: 0.8966 (ptp) REVERT: D 50 LEU cc_start: 0.9125 (tt) cc_final: 0.8849 (tt) REVERT: D 121 MET cc_start: 0.8371 (tpp) cc_final: 0.7532 (tpp) REVERT: D 137 ILE cc_start: 0.9311 (tt) cc_final: 0.9008 (tp) REVERT: D 151 MET cc_start: 0.6359 (mtt) cc_final: 0.6107 (ttp) REVERT: D 216 GLU cc_start: 0.9005 (pp20) cc_final: 0.8605 (pp20) REVERT: D 290 PHE cc_start: 0.8914 (m-80) cc_final: 0.8701 (m-80) REVERT: D 310 GLN cc_start: 0.8719 (mp10) cc_final: 0.8481 (mp10) REVERT: D 354 LYS cc_start: 0.8534 (tttp) cc_final: 0.7716 (mttt) REVERT: D 356 ASP cc_start: 0.9199 (m-30) cc_final: 0.8817 (t0) REVERT: D 360 ARG cc_start: 0.8429 (mpt180) cc_final: 0.8123 (mpt-90) REVERT: D 389 ASN cc_start: 0.8570 (m-40) cc_final: 0.8253 (m-40) REVERT: D 415 MET cc_start: 0.6276 (pmm) cc_final: 0.5085 (pmm) REVERT: D 418 SER cc_start: 0.8923 (t) cc_final: 0.8393 (p) REVERT: D 479 HIS cc_start: 0.9307 (m90) cc_final: 0.9098 (m90) REVERT: D 496 TYR cc_start: 0.7981 (m-80) cc_final: 0.7560 (m-80) REVERT: D 539 ARG cc_start: 0.7653 (ttm170) cc_final: 0.6994 (ttm170) REVERT: D 543 TYR cc_start: 0.8730 (p90) cc_final: 0.8167 (p90) REVERT: D 545 VAL cc_start: 0.8818 (t) cc_final: 0.7718 (t) REVERT: D 552 ILE cc_start: 0.9110 (pt) cc_final: 0.8594 (pt) REVERT: D 572 PHE cc_start: 0.8489 (p90) cc_final: 0.8119 (p90) REVERT: D 798 MET cc_start: 0.8278 (mpp) cc_final: 0.8051 (mpp) REVERT: D 858 TRP cc_start: 0.7681 (m-90) cc_final: 0.7279 (m-90) REVERT: D 877 LEU cc_start: 0.8930 (mt) cc_final: 0.8506 (tt) REVERT: D 901 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8470 (mmtt) REVERT: D 933 LEU cc_start: 0.9481 (mt) cc_final: 0.9273 (mt) REVERT: D 935 LEU cc_start: 0.7512 (mt) cc_final: 0.7132 (tp) REVERT: D 965 LEU cc_start: 0.9152 (mt) cc_final: 0.8746 (mt) REVERT: D 985 TYR cc_start: 0.9220 (m-80) cc_final: 0.8787 (m-80) REVERT: D 1205 GLU cc_start: 0.8274 (pt0) cc_final: 0.7989 (tt0) REVERT: D 1223 PRO cc_start: 0.6051 (Cg_exo) cc_final: 0.5588 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8446 (p) cc_final: 0.7982 (t) REVERT: D 1227 ASP cc_start: 0.9109 (m-30) cc_final: 0.8866 (p0) REVERT: D 1241 GLN cc_start: 0.7788 (mp-120) cc_final: 0.7436 (mp10) REVERT: D 1328 LEU cc_start: 0.9520 (tp) cc_final: 0.9075 (tp) REVERT: D 1330 TYR cc_start: 0.8941 (p90) cc_final: 0.8717 (p90) REVERT: D 1331 ASN cc_start: 0.6437 (m110) cc_final: 0.4003 (m110) REVERT: D 1333 LEU cc_start: 0.9075 (tp) cc_final: 0.8874 (tp) outliers start: 5 outliers final: 0 residues processed: 888 average time/residue: 0.2404 time to fit residues: 353.2805 Evaluate side-chains 718 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 302 optimal weight: 20.0000 chunk 430 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 447 optimal weight: 8.9990 chunk 40 optimal weight: 0.0870 chunk 210 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 6.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN B 156 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN B1072 GLN B1089 ASN ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN C1051 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1072 GLN D1089 ASN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064109 restraints weight = 183713.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066471 restraints weight = 129782.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068347 restraints weight = 98724.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.069849 restraints weight = 78587.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071052 restraints weight = 64864.062| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 41259 Z= 0.327 Angle : 0.962 12.540 56144 Z= 0.492 Chirality : 0.054 0.391 6471 Planarity : 0.007 0.069 7166 Dihedral : 6.667 35.716 5444 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.76 % Favored : 88.16 % Rotamer: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.11), residues: 5084 helix: -0.67 (0.16), residues: 866 sheet: -2.07 (0.11), residues: 1759 loop : -3.23 (0.11), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 787 TYR 0.049 0.003 TYR B1152 PHE 0.042 0.003 PHE A1126 TRP 0.040 0.004 TRP B 436 HIS 0.012 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.33 (41179) covalent geometry : angle 0.94414 / 0.49 (55948) SS BOND : bond 0.01676 / 1.04 ( 44) SS BOND : angle 2.62296 / 1.66 ( 88) hydrogen bonds : bond 0.05403 / 3.63 ( 536) hydrogen bonds : angle 5.49349 / 3.79 ( 1608) link_BETA1-4 : bond 0.00948 / 0.47 ( 8) link_BETA1-4 : angle 2.85939 / 1.68 ( 24) link_NAG-ASN : bond 0.01237 / 0.79 ( 28) link_NAG-ASN : angle 3.91685 / 2.60 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 819 time to evaluate : 1.564 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: 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: 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: 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: 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: A 32 MET cc_start: 0.9435 (ttt) cc_final: 0.9105 (ttt) REVERT: A 50 LEU cc_start: 0.9356 (tt) cc_final: 0.8809 (mm) REVERT: A 121 MET cc_start: 0.8940 (mmt) cc_final: 0.8650 (mpp) REVERT: A 137 ILE cc_start: 0.8942 (tt) cc_final: 0.8730 (tt) REVERT: A 229 PHE cc_start: 0.8756 (p90) cc_final: 0.8475 (p90) REVERT: A 256 TYR cc_start: 0.7872 (t80) cc_final: 0.6948 (t80) REVERT: A 271 LYS cc_start: 0.8021 (mptt) cc_final: 0.7575 (mptt) REVERT: A 290 PHE cc_start: 0.9453 (m-80) cc_final: 0.9099 (m-80) REVERT: A 373 ASP cc_start: 0.8149 (t0) cc_final: 0.7750 (t0) REVERT: A 428 ARG cc_start: 0.6116 (mpt180) cc_final: 0.5462 (mtt180) REVERT: A 462 GLU cc_start: 0.7763 (pt0) cc_final: 0.7402 (pm20) REVERT: A 464 MET cc_start: 0.9549 (tpt) cc_final: 0.9136 (ttm) REVERT: A 500 MET cc_start: 0.4358 (mmp) cc_final: 0.2829 (ttt) REVERT: A 523 HIS cc_start: 0.9068 (m-70) cc_final: 0.8762 (m-70) REVERT: A 542 ILE cc_start: 0.9440 (mt) cc_final: 0.9169 (tp) REVERT: A 564 LEU cc_start: 0.9350 (mm) cc_final: 0.9066 (tp) REVERT: A 582 HIS cc_start: 0.9291 (t70) cc_final: 0.8854 (p-80) REVERT: A 627 LEU cc_start: 0.9291 (mm) cc_final: 0.8866 (mp) REVERT: A 666 MET cc_start: 0.9149 (ttm) cc_final: 0.8613 (ptm) REVERT: A 669 PHE cc_start: 0.8613 (m-10) cc_final: 0.8365 (m-80) REVERT: A 671 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9320 (mm-30) REVERT: A 787 ARG cc_start: 0.9102 (ptp90) cc_final: 0.8680 (ptm-80) REVERT: A 800 TYR cc_start: 0.9081 (p90) cc_final: 0.8752 (p90) REVERT: A 870 PHE cc_start: 0.8946 (m-80) cc_final: 0.8425 (m-80) REVERT: A 968 MET cc_start: 0.7789 (tpt) cc_final: 0.7027 (pmm) REVERT: A 975 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8579 (tp-100) REVERT: A 988 ASP cc_start: 0.9097 (m-30) cc_final: 0.8646 (m-30) REVERT: A 1020 HIS cc_start: 0.8213 (m-70) cc_final: 0.7440 (m-70) REVERT: A 1057 PHE cc_start: 0.8765 (t80) cc_final: 0.8466 (t80) REVERT: A 1132 TRP cc_start: 0.8801 (t60) cc_final: 0.7798 (t60) REVERT: A 1133 LYS cc_start: 0.9471 (ttmt) cc_final: 0.9228 (tppt) REVERT: A 1150 LEU cc_start: 0.9515 (mm) cc_final: 0.9206 (pp) REVERT: A 1154 PHE cc_start: 0.9220 (m-80) cc_final: 0.8290 (m-80) REVERT: A 1165 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 1214 LEU cc_start: 0.9405 (mt) cc_final: 0.9204 (mt) REVERT: A 1323 TYR cc_start: 0.8439 (t80) cc_final: 0.8038 (t80) REVERT: B 32 MET cc_start: 0.9176 (tpt) cc_final: 0.8973 (tpt) REVERT: B 121 MET cc_start: 0.8610 (tpp) cc_final: 0.7937 (tpp) REVERT: B 151 MET cc_start: 0.6752 (mtt) cc_final: 0.6252 (ttp) REVERT: B 290 PHE cc_start: 0.9160 (m-80) cc_final: 0.8791 (m-80) REVERT: B 291 SER cc_start: 0.8781 (p) cc_final: 0.8318 (t) REVERT: B 354 LYS cc_start: 0.8759 (tttp) cc_final: 0.7856 (mttt) REVERT: B 356 ASP cc_start: 0.9167 (m-30) cc_final: 0.8898 (t0) REVERT: B 360 ARG cc_start: 0.8864 (mpt180) cc_final: 0.8478 (mpt-90) REVERT: B 461 LEU cc_start: 0.9194 (mm) cc_final: 0.8954 (mm) REVERT: B 496 TYR cc_start: 0.8054 (m-80) cc_final: 0.7657 (m-80) REVERT: B 543 TYR cc_start: 0.8728 (p90) cc_final: 0.8179 (p90) REVERT: B 545 VAL cc_start: 0.8888 (t) cc_final: 0.8497 (t) REVERT: B 552 ILE cc_start: 0.9395 (pt) cc_final: 0.9041 (pt) REVERT: B 554 ASP cc_start: 0.7507 (t0) cc_final: 0.7288 (t0) REVERT: B 669 PHE cc_start: 0.8764 (m-80) cc_final: 0.8543 (m-80) REVERT: B 737 GLU cc_start: 0.8636 (pm20) cc_final: 0.8412 (pp20) REVERT: B 870 PHE cc_start: 0.9362 (t80) cc_final: 0.9136 (t80) REVERT: B 877 LEU cc_start: 0.8961 (mt) cc_final: 0.8509 (tt) REVERT: B 965 LEU cc_start: 0.9341 (mt) cc_final: 0.9039 (mt) REVERT: B 985 TYR cc_start: 0.9199 (m-80) cc_final: 0.8867 (m-80) REVERT: B 1028 PHE cc_start: 0.9412 (m-10) cc_final: 0.9182 (m-80) REVERT: B 1156 LEU cc_start: 0.8114 (mm) cc_final: 0.7781 (mm) REVERT: B 1205 GLU cc_start: 0.8424 (pt0) cc_final: 0.8041 (tt0) REVERT: B 1223 PRO cc_start: 0.7296 (Cg_exo) cc_final: 0.6994 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8982 (p) cc_final: 0.8565 (t) REVERT: B 1241 GLN cc_start: 0.7543 (mp-120) cc_final: 0.7153 (mp10) REVERT: B 1328 LEU cc_start: 0.9469 (tp) cc_final: 0.8935 (tp) REVERT: B 1330 TYR cc_start: 0.9068 (p90) cc_final: 0.8796 (p90) REVERT: C 32 MET cc_start: 0.9451 (ttt) cc_final: 0.9124 (ttt) REVERT: C 50 LEU cc_start: 0.9381 (tt) cc_final: 0.8852 (mm) REVERT: C 121 MET cc_start: 0.8980 (mmt) cc_final: 0.8670 (mpp) REVERT: C 137 ILE cc_start: 0.8938 (tt) cc_final: 0.8727 (tt) REVERT: C 209 LYS cc_start: 0.9308 (mtmt) cc_final: 0.8543 (mmtm) REVERT: C 229 PHE cc_start: 0.8751 (p90) cc_final: 0.8472 (p90) REVERT: C 256 TYR cc_start: 0.7856 (t80) cc_final: 0.6949 (t80) REVERT: C 290 PHE cc_start: 0.9443 (m-80) cc_final: 0.9091 (m-80) REVERT: C 373 ASP cc_start: 0.8163 (t0) cc_final: 0.7727 (t0) REVERT: C 428 ARG cc_start: 0.6018 (mpt180) cc_final: 0.5406 (mtt180) REVERT: C 462 GLU cc_start: 0.7763 (pt0) cc_final: 0.7408 (pm20) REVERT: C 464 MET cc_start: 0.9541 (tpt) cc_final: 0.9127 (ttm) REVERT: C 500 MET cc_start: 0.4448 (mmp) cc_final: 0.2986 (ttt) REVERT: C 523 HIS cc_start: 0.9072 (m-70) cc_final: 0.8768 (m-70) REVERT: C 542 ILE cc_start: 0.9441 (mt) cc_final: 0.9174 (tp) REVERT: C 564 LEU cc_start: 0.9353 (mm) cc_final: 0.9079 (tp) REVERT: C 582 HIS cc_start: 0.9288 (t70) cc_final: 0.8847 (p-80) REVERT: C 666 MET cc_start: 0.9163 (ttm) cc_final: 0.8679 (ptm) REVERT: C 669 PHE cc_start: 0.8619 (m-10) cc_final: 0.8373 (m-80) REVERT: C 787 ARG cc_start: 0.9099 (ptp90) cc_final: 0.8680 (ptm-80) REVERT: C 796 LEU cc_start: 0.9034 (pp) cc_final: 0.8805 (pp) REVERT: C 800 TYR cc_start: 0.8963 (p90) cc_final: 0.8735 (p90) REVERT: C 968 MET cc_start: 0.7786 (tpt) cc_final: 0.7027 (pmm) REVERT: C 975 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8547 (tp-100) REVERT: C 988 ASP cc_start: 0.9299 (m-30) cc_final: 0.9012 (m-30) REVERT: C 1020 HIS cc_start: 0.8206 (m-70) cc_final: 0.7427 (m-70) REVERT: C 1057 PHE cc_start: 0.8784 (t80) cc_final: 0.8438 (t80) REVERT: C 1132 TRP cc_start: 0.8836 (t60) cc_final: 0.7869 (t60) REVERT: C 1133 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9217 (tppt) REVERT: C 1150 LEU cc_start: 0.9523 (mm) cc_final: 0.9213 (pp) REVERT: C 1154 PHE cc_start: 0.9225 (m-80) cc_final: 0.8288 (m-80) REVERT: C 1165 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 1214 LEU cc_start: 0.9394 (mt) cc_final: 0.9192 (mt) REVERT: C 1323 TYR cc_start: 0.8480 (t80) cc_final: 0.8093 (t80) REVERT: D 32 MET cc_start: 0.9090 (tpt) cc_final: 0.8864 (tpt) REVERT: D 54 LEU cc_start: 0.8091 (tp) cc_final: 0.7848 (tp) REVERT: D 121 MET cc_start: 0.8568 (tpp) cc_final: 0.7892 (tpp) REVERT: D 151 MET cc_start: 0.6738 (mtt) cc_final: 0.6255 (ttp) REVERT: D 290 PHE cc_start: 0.9168 (m-80) cc_final: 0.8776 (m-80) REVERT: D 291 SER cc_start: 0.8775 (p) cc_final: 0.8306 (t) REVERT: D 354 LYS cc_start: 0.8766 (tttp) cc_final: 0.7863 (mttt) REVERT: D 356 ASP cc_start: 0.9172 (m-30) cc_final: 0.8898 (t0) REVERT: D 360 ARG cc_start: 0.8875 (mpt180) cc_final: 0.8479 (mpt-90) REVERT: D 461 LEU cc_start: 0.9198 (mm) cc_final: 0.8965 (mm) REVERT: D 496 TYR cc_start: 0.8081 (m-80) cc_final: 0.7698 (m-80) REVERT: D 543 TYR cc_start: 0.8746 (p90) cc_final: 0.8192 (p90) REVERT: D 545 VAL cc_start: 0.8752 (t) cc_final: 0.8045 (t) REVERT: D 552 ILE cc_start: 0.9395 (pt) cc_final: 0.9037 (pt) REVERT: D 554 ASP cc_start: 0.7511 (t0) cc_final: 0.7288 (t0) REVERT: D 669 PHE cc_start: 0.8765 (m-80) cc_final: 0.8547 (m-80) REVERT: D 688 MET cc_start: 0.8349 (ppp) cc_final: 0.8051 (ppp) REVERT: D 796 LEU cc_start: 0.8714 (pp) cc_final: 0.8139 (pp) REVERT: D 870 PHE cc_start: 0.9408 (t80) cc_final: 0.9161 (t80) REVERT: D 877 LEU cc_start: 0.8963 (mt) cc_final: 0.8514 (tt) REVERT: D 965 LEU cc_start: 0.9339 (mt) cc_final: 0.9089 (mt) REVERT: D 985 TYR cc_start: 0.9148 (m-80) cc_final: 0.8710 (m-80) REVERT: D 1028 PHE cc_start: 0.9406 (m-10) cc_final: 0.9176 (m-80) REVERT: D 1156 LEU cc_start: 0.8106 (mm) cc_final: 0.7774 (mm) REVERT: D 1205 GLU cc_start: 0.8379 (pt0) cc_final: 0.7984 (tt0) REVERT: D 1223 PRO cc_start: 0.7259 (Cg_exo) cc_final: 0.6957 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8971 (p) cc_final: 0.8561 (t) REVERT: D 1241 GLN cc_start: 0.7588 (mp-120) cc_final: 0.7214 (mp10) REVERT: D 1330 TYR cc_start: 0.9100 (p90) cc_final: 0.8887 (p90) REVERT: D 1333 LEU cc_start: 0.9207 (tp) cc_final: 0.8995 (tp) outliers start: 3 outliers final: 0 residues processed: 820 average time/residue: 0.2383 time to fit residues: 324.3082 Evaluate side-chains 636 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 425 optimal weight: 4.9990 chunk 182 optimal weight: 0.3980 chunk 180 optimal weight: 1.9990 chunk 395 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 340 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 474 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN A 976 ASN ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 321 HIS B 327 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN B1072 GLN B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS C 474 GLN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN C 976 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN D1017 ASN D1072 GLN D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.088004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.067122 restraints weight = 172453.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069720 restraints weight = 120321.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.071787 restraints weight = 90864.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.073401 restraints weight = 71796.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074688 restraints weight = 59132.137| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41259 Z= 0.166 Angle : 0.799 12.065 56144 Z= 0.398 Chirality : 0.051 0.417 6471 Planarity : 0.006 0.084 7166 Dihedral : 6.099 35.845 5444 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.44 % Favored : 89.48 % Rotamer: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.11), residues: 5084 helix: -0.18 (0.17), residues: 882 sheet: -1.85 (0.11), residues: 1820 loop : -3.10 (0.11), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 684 TYR 0.028 0.002 TYR B1152 PHE 0.068 0.002 PHE C1049 TRP 0.038 0.003 TRP D 436 HIS 0.008 0.001 HIS D 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (41179) covalent geometry : angle 0.78220 / 0.39 (55948) SS BOND : bond 0.00825 / 0.43 ( 44) SS BOND : angle 2.18370 / 1.39 ( 88) hydrogen bonds : bond 0.04913 / 3.29 ( 536) hydrogen bonds : angle 4.99008 / 3.42 ( 1608) link_BETA1-4 : bond 0.01012 / 0.64 ( 8) link_BETA1-4 : angle 2.22540 / 1.40 ( 24) link_NAG-ASN : bond 0.00819 / 0.54 ( 28) link_NAG-ASN : angle 3.56384 / 2.34 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 839 time to evaluate : 1.687 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: 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: 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: 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: 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: A 32 MET cc_start: 0.9436 (ttt) cc_final: 0.9109 (ttt) REVERT: A 50 LEU cc_start: 0.9419 (tt) cc_final: 0.8496 (mm) REVERT: A 121 MET cc_start: 0.9051 (mmt) cc_final: 0.8632 (mpp) REVERT: A 151 MET cc_start: 0.4036 (ttm) cc_final: 0.3812 (ttm) REVERT: A 183 LEU cc_start: 0.8536 (tp) cc_final: 0.8328 (tp) REVERT: A 209 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8441 (mmtm) REVERT: A 251 CYS cc_start: 0.8367 (m) cc_final: 0.8009 (t) REVERT: A 271 LYS cc_start: 0.7990 (mptt) cc_final: 0.7734 (mmtt) REVERT: A 290 PHE cc_start: 0.9459 (m-80) cc_final: 0.9097 (m-80) REVERT: A 373 ASP cc_start: 0.8151 (t0) cc_final: 0.7709 (t0) REVERT: A 428 ARG cc_start: 0.5658 (mpt180) cc_final: 0.5122 (mtp180) REVERT: A 462 GLU cc_start: 0.7713 (pt0) cc_final: 0.7354 (pm20) REVERT: A 523 HIS cc_start: 0.9160 (m-70) cc_final: 0.8893 (m-70) REVERT: A 564 LEU cc_start: 0.9358 (mm) cc_final: 0.9043 (tp) REVERT: A 582 HIS cc_start: 0.9270 (t70) cc_final: 0.8886 (p-80) REVERT: A 626 ASP cc_start: 0.8977 (p0) cc_final: 0.8244 (t0) REVERT: A 627 LEU cc_start: 0.8999 (mm) cc_final: 0.8625 (mp) REVERT: A 666 MET cc_start: 0.9109 (ttm) cc_final: 0.8781 (ptm) REVERT: A 669 PHE cc_start: 0.8487 (m-10) cc_final: 0.8186 (m-10) REVERT: A 688 MET cc_start: 0.8803 (ppp) cc_final: 0.8385 (ppp) REVERT: A 800 TYR cc_start: 0.9023 (p90) cc_final: 0.8800 (p90) REVERT: A 965 LEU cc_start: 0.9217 (tt) cc_final: 0.8958 (tt) REVERT: A 975 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8484 (tp-100) REVERT: A 983 ASN cc_start: 0.9416 (m-40) cc_final: 0.9146 (m110) REVERT: A 988 ASP cc_start: 0.9085 (m-30) cc_final: 0.8625 (m-30) REVERT: A 1028 PHE cc_start: 0.8556 (m-10) cc_final: 0.8133 (t80) REVERT: A 1057 PHE cc_start: 0.8624 (t80) cc_final: 0.8394 (t80) REVERT: A 1076 ASP cc_start: 0.8845 (p0) cc_final: 0.8535 (m-30) REVERT: A 1132 TRP cc_start: 0.8763 (t60) cc_final: 0.7873 (t60) REVERT: A 1133 LYS cc_start: 0.9459 (ttmt) cc_final: 0.9214 (tppt) REVERT: A 1144 VAL cc_start: 0.8360 (p) cc_final: 0.8024 (m) REVERT: A 1150 LEU cc_start: 0.9525 (mm) cc_final: 0.9232 (pp) REVERT: A 1154 PHE cc_start: 0.9205 (m-80) cc_final: 0.8188 (m-80) REVERT: A 1165 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 1323 TYR cc_start: 0.8253 (t80) cc_final: 0.7793 (t80) REVERT: B 32 MET cc_start: 0.9118 (tpt) cc_final: 0.8842 (tpt) REVERT: B 121 MET cc_start: 0.8615 (tpp) cc_final: 0.8100 (tpt) REVERT: B 134 ASP cc_start: 0.8820 (t70) cc_final: 0.8605 (t70) REVERT: B 179 GLN cc_start: 0.8264 (pp30) cc_final: 0.8050 (pp30) REVERT: B 290 PHE cc_start: 0.8990 (m-80) cc_final: 0.8675 (m-80) REVERT: B 291 SER cc_start: 0.8922 (p) cc_final: 0.8509 (t) REVERT: B 354 LYS cc_start: 0.8624 (tttp) cc_final: 0.7707 (mttt) REVERT: B 356 ASP cc_start: 0.9231 (m-30) cc_final: 0.8874 (t0) REVERT: B 360 ARG cc_start: 0.8675 (mpt180) cc_final: 0.8403 (mpt-90) REVERT: B 415 MET cc_start: 0.6674 (pmm) cc_final: 0.5179 (pmm) REVERT: B 418 SER cc_start: 0.9099 (t) cc_final: 0.8884 (t) REVERT: B 461 LEU cc_start: 0.9171 (mm) cc_final: 0.8943 (mm) REVERT: B 496 TYR cc_start: 0.7921 (m-80) cc_final: 0.7550 (m-80) REVERT: B 539 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6560 (ttt180) REVERT: B 543 TYR cc_start: 0.8662 (p90) cc_final: 0.8109 (p90) REVERT: B 550 ASP cc_start: 0.9204 (m-30) cc_final: 0.8947 (t70) REVERT: B 552 ILE cc_start: 0.9318 (pt) cc_final: 0.8928 (pt) REVERT: B 554 ASP cc_start: 0.7072 (t0) cc_final: 0.6768 (t0) REVERT: B 669 PHE cc_start: 0.8715 (m-80) cc_final: 0.8463 (m-80) REVERT: B 673 MET cc_start: 0.9148 (tpt) cc_final: 0.8907 (tpp) REVERT: B 870 PHE cc_start: 0.9344 (t80) cc_final: 0.9117 (t80) REVERT: B 877 LEU cc_start: 0.8968 (mt) cc_final: 0.8533 (tt) REVERT: B 965 LEU cc_start: 0.9307 (mt) cc_final: 0.9026 (mt) REVERT: B 985 TYR cc_start: 0.9071 (m-80) cc_final: 0.8796 (m-80) REVERT: B 1067 LEU cc_start: 0.8716 (mt) cc_final: 0.8495 (mt) REVERT: B 1072 GLN cc_start: 0.9413 (mt0) cc_final: 0.8946 (tm-30) REVERT: B 1165 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8863 (tt0) REVERT: B 1205 GLU cc_start: 0.8366 (pt0) cc_final: 0.8006 (tt0) REVERT: B 1241 GLN cc_start: 0.7497 (mp-120) cc_final: 0.7123 (mp10) REVERT: B 1328 LEU cc_start: 0.9446 (tp) cc_final: 0.9008 (tp) REVERT: B 1330 TYR cc_start: 0.9061 (p90) cc_final: 0.8646 (p90) REVERT: B 1331 ASN cc_start: 0.6124 (m110) cc_final: 0.4044 (m110) REVERT: C 32 MET cc_start: 0.9453 (ttt) cc_final: 0.9142 (ttt) REVERT: C 50 LEU cc_start: 0.9442 (tt) cc_final: 0.8529 (mm) REVERT: C 121 MET cc_start: 0.9080 (mmt) cc_final: 0.8655 (mpp) REVERT: C 151 MET cc_start: 0.4070 (ttm) cc_final: 0.3840 (ttm) REVERT: C 209 LYS cc_start: 0.9267 (mtmt) cc_final: 0.8428 (mmtm) REVERT: C 251 CYS cc_start: 0.8411 (m) cc_final: 0.8036 (t) REVERT: C 271 LYS cc_start: 0.7641 (mptt) cc_final: 0.7327 (mmtt) REVERT: C 290 PHE cc_start: 0.9468 (m-80) cc_final: 0.9077 (m-80) REVERT: C 309 PHE cc_start: 0.9087 (m-80) cc_final: 0.8676 (m-80) REVERT: C 373 ASP cc_start: 0.8201 (t0) cc_final: 0.7767 (t0) REVERT: C 428 ARG cc_start: 0.5657 (mpt180) cc_final: 0.5139 (mtp180) REVERT: C 462 GLU cc_start: 0.7713 (pt0) cc_final: 0.7373 (pm20) REVERT: C 523 HIS cc_start: 0.9167 (m-70) cc_final: 0.8900 (m-70) REVERT: C 564 LEU cc_start: 0.9360 (mm) cc_final: 0.9049 (tp) REVERT: C 582 HIS cc_start: 0.9273 (t70) cc_final: 0.8889 (p-80) REVERT: C 626 ASP cc_start: 0.8968 (p0) cc_final: 0.8298 (t0) REVERT: C 666 MET cc_start: 0.9068 (ttm) cc_final: 0.8772 (ptm) REVERT: C 669 PHE cc_start: 0.8535 (m-10) cc_final: 0.8307 (m-10) REVERT: C 688 MET cc_start: 0.8802 (ppp) cc_final: 0.8386 (ppp) REVERT: C 931 LEU cc_start: 0.8868 (tp) cc_final: 0.8267 (tt) REVERT: C 975 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8491 (tp-100) REVERT: C 988 ASP cc_start: 0.8978 (m-30) cc_final: 0.8765 (m-30) REVERT: C 1028 PHE cc_start: 0.8540 (m-10) cc_final: 0.8126 (t80) REVERT: C 1057 PHE cc_start: 0.8703 (t80) cc_final: 0.8273 (t80) REVERT: C 1144 VAL cc_start: 0.8361 (p) cc_final: 0.8019 (m) REVERT: C 1150 LEU cc_start: 0.9518 (mm) cc_final: 0.9185 (pp) REVERT: C 1154 PHE cc_start: 0.9216 (m-80) cc_final: 0.8149 (m-80) REVERT: C 1165 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 1323 TYR cc_start: 0.8268 (t80) cc_final: 0.7829 (t80) REVERT: D 32 MET cc_start: 0.9035 (tpt) cc_final: 0.8737 (tpt) REVERT: D 121 MET cc_start: 0.8578 (tpp) cc_final: 0.7899 (tpp) REVERT: D 179 GLN cc_start: 0.8275 (pp30) cc_final: 0.8056 (pp30) REVERT: D 290 PHE cc_start: 0.8978 (m-80) cc_final: 0.8765 (m-80) REVERT: D 291 SER cc_start: 0.8912 (p) cc_final: 0.8497 (t) REVERT: D 356 ASP cc_start: 0.9250 (m-30) cc_final: 0.8925 (t0) REVERT: D 360 ARG cc_start: 0.8693 (mpt180) cc_final: 0.8408 (mpt-90) REVERT: D 389 ASN cc_start: 0.8923 (m-40) cc_final: 0.8720 (m-40) REVERT: D 415 MET cc_start: 0.6667 (pmm) cc_final: 0.5177 (pmm) REVERT: D 418 SER cc_start: 0.9096 (t) cc_final: 0.8889 (t) REVERT: D 479 HIS cc_start: 0.9190 (m90) cc_final: 0.8989 (m90) REVERT: D 496 TYR cc_start: 0.7884 (m-80) cc_final: 0.7554 (m-80) REVERT: D 539 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6582 (ttt180) REVERT: D 543 TYR cc_start: 0.8617 (p90) cc_final: 0.7978 (p90) REVERT: D 545 VAL cc_start: 0.8753 (t) cc_final: 0.7855 (t) REVERT: D 552 ILE cc_start: 0.9339 (pt) cc_final: 0.8959 (pt) REVERT: D 554 ASP cc_start: 0.7103 (t0) cc_final: 0.6799 (t0) REVERT: D 572 PHE cc_start: 0.8499 (p90) cc_final: 0.8108 (p90) REVERT: D 669 PHE cc_start: 0.8712 (m-80) cc_final: 0.8465 (m-80) REVERT: D 673 MET cc_start: 0.9134 (tpt) cc_final: 0.8905 (tpp) REVERT: D 798 MET cc_start: 0.8227 (mpp) cc_final: 0.7726 (mpp) REVERT: D 877 LEU cc_start: 0.8965 (mt) cc_final: 0.8531 (tt) REVERT: D 965 LEU cc_start: 0.9329 (mt) cc_final: 0.9115 (mt) REVERT: D 985 TYR cc_start: 0.9072 (m-80) cc_final: 0.8744 (m-80) REVERT: D 1067 LEU cc_start: 0.8751 (mt) cc_final: 0.8532 (mt) REVERT: D 1072 GLN cc_start: 0.9423 (mt0) cc_final: 0.9042 (tm-30) REVERT: D 1165 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8860 (tt0) REVERT: D 1205 GLU cc_start: 0.8380 (pt0) cc_final: 0.8046 (tt0) REVERT: D 1241 GLN cc_start: 0.7543 (mp-120) cc_final: 0.7179 (mp10) REVERT: D 1328 LEU cc_start: 0.9520 (tp) cc_final: 0.8873 (tp) REVERT: D 1330 TYR cc_start: 0.9012 (p90) cc_final: 0.8697 (p90) REVERT: D 1331 ASN cc_start: 0.6108 (m110) cc_final: 0.3953 (m110) outliers start: 6 outliers final: 0 residues processed: 843 average time/residue: 0.2223 time to fit residues: 312.2646 Evaluate side-chains 678 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 252 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 489 optimal weight: 9.9990 chunk 418 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 352 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 444 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 HIS B 406 GLN B 477 GLN B 479 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 441 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN D 477 GLN D 479 HIS ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1036 GLN D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.089182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068023 restraints weight = 170168.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.070743 restraints weight = 117785.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072859 restraints weight = 88276.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074531 restraints weight = 69641.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.075853 restraints weight = 57078.413| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41259 Z= 0.146 Angle : 0.774 12.080 56144 Z= 0.383 Chirality : 0.050 0.385 6471 Planarity : 0.006 0.080 7166 Dihedral : 5.838 38.292 5444 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.29 % Favored : 89.67 % Rotamer: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.86 (0.11), residues: 5084 helix: 0.04 (0.17), residues: 882 sheet: -1.58 (0.12), residues: 1801 loop : -2.94 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1081 TYR 0.032 0.002 TYR D1152 PHE 0.064 0.002 PHE A1049 TRP 0.067 0.003 TRP B 739 HIS 0.006 0.001 HIS C1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (41179) covalent geometry : angle 0.75997 / 0.38 (55948) SS BOND : bond 0.00533 / 0.30 ( 44) SS BOND : angle 2.04849 / 1.31 ( 88) hydrogen bonds : bond 0.04794 / 3.23 ( 536) hydrogen bonds : angle 4.86245 / 3.34 ( 1608) link_BETA1-4 : bond 0.00984 / 0.54 ( 8) link_BETA1-4 : angle 2.32081 / 1.42 ( 24) link_NAG-ASN : bond 0.00734 / 0.47 ( 28) link_NAG-ASN : angle 3.17446 / 2.11 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 834 time to evaluate : 1.563 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: 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: 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: 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: 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: 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: A 32 MET cc_start: 0.9428 (ttt) cc_final: 0.9055 (ttt) REVERT: A 50 LEU cc_start: 0.9369 (tt) cc_final: 0.8353 (mm) REVERT: A 121 MET cc_start: 0.9040 (mmt) cc_final: 0.8579 (mpp) REVERT: A 137 ILE cc_start: 0.8662 (tt) cc_final: 0.8395 (tt) REVERT: A 151 MET cc_start: 0.4182 (ttm) cc_final: 0.3898 (ttm) REVERT: A 209 LYS cc_start: 0.9284 (mtmt) cc_final: 0.8409 (mmtm) REVERT: A 251 CYS cc_start: 0.8335 (m) cc_final: 0.7947 (t) REVERT: A 290 PHE cc_start: 0.9435 (m-80) cc_final: 0.8993 (m-80) REVERT: A 373 ASP cc_start: 0.8113 (t0) cc_final: 0.7843 (t0) REVERT: A 425 TYR cc_start: 0.5129 (t80) cc_final: 0.4833 (t80) REVERT: A 428 ARG cc_start: 0.5545 (mpt180) cc_final: 0.5111 (mtp180) REVERT: A 462 GLU cc_start: 0.7674 (pt0) cc_final: 0.7315 (pm20) REVERT: A 523 HIS cc_start: 0.9148 (m-70) cc_final: 0.8891 (m-70) REVERT: A 542 ILE cc_start: 0.9326 (mp) cc_final: 0.8842 (tp) REVERT: A 564 LEU cc_start: 0.9391 (mm) cc_final: 0.9043 (tp) REVERT: A 573 SER cc_start: 0.9320 (t) cc_final: 0.9094 (p) REVERT: A 582 HIS cc_start: 0.9225 (t70) cc_final: 0.8738 (p-80) REVERT: A 626 ASP cc_start: 0.8982 (p0) cc_final: 0.8202 (t0) REVERT: A 627 LEU cc_start: 0.9038 (mm) cc_final: 0.8769 (mp) REVERT: A 666 MET cc_start: 0.9008 (ttm) cc_final: 0.8536 (ptp) REVERT: A 669 PHE cc_start: 0.8476 (m-10) cc_final: 0.8211 (m-10) REVERT: A 671 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9301 (mm-30) REVERT: A 798 MET cc_start: 0.8563 (ppp) cc_final: 0.8135 (ppp) REVERT: A 965 LEU cc_start: 0.9185 (tt) cc_final: 0.8962 (tt) REVERT: A 975 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8417 (tp-100) REVERT: A 983 ASN cc_start: 0.9426 (m-40) cc_final: 0.9073 (m110) REVERT: A 1020 HIS cc_start: 0.8886 (t-90) cc_final: 0.8495 (t-90) REVERT: A 1028 PHE cc_start: 0.8534 (m-10) cc_final: 0.8145 (t80) REVERT: A 1057 PHE cc_start: 0.8622 (t80) cc_final: 0.8212 (t80) REVERT: A 1076 ASP cc_start: 0.8854 (p0) cc_final: 0.8358 (m-30) REVERT: A 1132 TRP cc_start: 0.8706 (t60) cc_final: 0.8303 (t60) REVERT: A 1144 VAL cc_start: 0.8399 (p) cc_final: 0.8027 (m) REVERT: A 1165 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 1214 LEU cc_start: 0.9277 (mt) cc_final: 0.9075 (mt) REVERT: A 1323 TYR cc_start: 0.8201 (t80) cc_final: 0.7676 (t80) REVERT: B 32 MET cc_start: 0.9057 (tpt) cc_final: 0.8768 (tpt) REVERT: B 121 MET cc_start: 0.8595 (tpp) cc_final: 0.8129 (tpt) REVERT: B 291 SER cc_start: 0.9003 (p) cc_final: 0.8636 (t) REVERT: B 310 GLN cc_start: 0.8754 (mp10) cc_final: 0.8481 (mp10) REVERT: B 354 LYS cc_start: 0.8592 (tttp) cc_final: 0.7712 (mttt) REVERT: B 356 ASP cc_start: 0.9210 (m-30) cc_final: 0.8905 (t0) REVERT: B 360 ARG cc_start: 0.8634 (mpt180) cc_final: 0.8289 (mpt-90) REVERT: B 363 ILE cc_start: 0.9232 (tp) cc_final: 0.9001 (tp) REVERT: B 389 ASN cc_start: 0.8871 (m-40) cc_final: 0.8648 (m-40) REVERT: B 394 TYR cc_start: 0.7967 (t80) cc_final: 0.7710 (t80) REVERT: B 415 MET cc_start: 0.6718 (pmm) cc_final: 0.4867 (pmm) REVERT: B 418 SER cc_start: 0.9022 (t) cc_final: 0.8737 (t) REVERT: B 461 LEU cc_start: 0.9120 (mm) cc_final: 0.8872 (mm) REVERT: B 479 HIS cc_start: 0.9253 (m-70) cc_final: 0.9006 (m90) REVERT: B 542 ILE cc_start: 0.9549 (mp) cc_final: 0.9189 (tp) REVERT: B 543 TYR cc_start: 0.8640 (p90) cc_final: 0.8124 (p90) REVERT: B 545 VAL cc_start: 0.8779 (t) cc_final: 0.8302 (t) REVERT: B 550 ASP cc_start: 0.9106 (m-30) cc_final: 0.8904 (m-30) REVERT: B 552 ILE cc_start: 0.9347 (pt) cc_final: 0.9051 (pt) REVERT: B 554 ASP cc_start: 0.6934 (t0) cc_final: 0.6726 (t0) REVERT: B 650 ILE cc_start: 0.6895 (mm) cc_final: 0.6684 (mm) REVERT: B 669 PHE cc_start: 0.8653 (m-80) cc_final: 0.8350 (m-80) REVERT: B 877 LEU cc_start: 0.8905 (mt) cc_final: 0.8449 (tt) REVERT: B 965 LEU cc_start: 0.9313 (mt) cc_final: 0.9091 (mt) REVERT: B 968 MET cc_start: 0.8289 (tpt) cc_final: 0.8044 (tpt) REVERT: B 985 TYR cc_start: 0.9112 (m-80) cc_final: 0.8817 (m-80) REVERT: B 1067 LEU cc_start: 0.8769 (mt) cc_final: 0.8568 (mt) REVERT: B 1165 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8870 (tt0) REVERT: B 1205 GLU cc_start: 0.8362 (pt0) cc_final: 0.8045 (tt0) REVERT: B 1241 GLN cc_start: 0.7388 (mp-120) cc_final: 0.7081 (mp10) REVERT: B 1330 TYR cc_start: 0.9011 (p90) cc_final: 0.8587 (p90) REVERT: C 32 MET cc_start: 0.9436 (ttt) cc_final: 0.9086 (ttt) REVERT: C 50 LEU cc_start: 0.9390 (tt) cc_final: 0.8388 (mm) REVERT: C 121 MET cc_start: 0.9058 (mmt) cc_final: 0.8590 (mpp) REVERT: C 137 ILE cc_start: 0.8631 (tt) cc_final: 0.8358 (tt) REVERT: C 151 MET cc_start: 0.4211 (ttm) cc_final: 0.3930 (ttm) REVERT: C 209 LYS cc_start: 0.9261 (mtmt) cc_final: 0.8367 (mmtm) REVERT: C 271 LYS cc_start: 0.7736 (mptt) cc_final: 0.7413 (mmtt) REVERT: C 290 PHE cc_start: 0.9431 (m-80) cc_final: 0.8987 (m-80) REVERT: C 373 ASP cc_start: 0.8095 (t0) cc_final: 0.7675 (t0) REVERT: C 425 TYR cc_start: 0.5101 (t80) cc_final: 0.4815 (t80) REVERT: C 428 ARG cc_start: 0.5535 (mpt180) cc_final: 0.4928 (mtt180) REVERT: C 462 GLU cc_start: 0.7606 (pt0) cc_final: 0.7286 (pm20) REVERT: C 523 HIS cc_start: 0.9148 (m-70) cc_final: 0.8893 (m-70) REVERT: C 542 ILE cc_start: 0.9335 (mp) cc_final: 0.9099 (tp) REVERT: C 564 LEU cc_start: 0.9398 (mm) cc_final: 0.9049 (tp) REVERT: C 573 SER cc_start: 0.9309 (t) cc_final: 0.9083 (p) REVERT: C 582 HIS cc_start: 0.9224 (t70) cc_final: 0.8732 (p-80) REVERT: C 626 ASP cc_start: 0.8952 (p0) cc_final: 0.8361 (t0) REVERT: C 666 MET cc_start: 0.8977 (ttm) cc_final: 0.8461 (ptp) REVERT: C 669 PHE cc_start: 0.8500 (m-10) cc_final: 0.8210 (m-10) REVERT: C 800 TYR cc_start: 0.8911 (p90) cc_final: 0.8692 (p90) REVERT: C 913 GLU cc_start: 0.9493 (pm20) cc_final: 0.9283 (pm20) REVERT: C 931 LEU cc_start: 0.8936 (tp) cc_final: 0.8365 (tt) REVERT: C 965 LEU cc_start: 0.9162 (tt) cc_final: 0.8922 (tt) REVERT: C 975 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8448 (tp-100) REVERT: C 983 ASN cc_start: 0.9329 (m-40) cc_final: 0.8987 (m110) REVERT: C 988 ASP cc_start: 0.9054 (m-30) cc_final: 0.8711 (m-30) REVERT: C 1020 HIS cc_start: 0.8884 (t-90) cc_final: 0.8515 (t-90) REVERT: C 1028 PHE cc_start: 0.8541 (m-10) cc_final: 0.8147 (t80) REVERT: C 1057 PHE cc_start: 0.8747 (t80) cc_final: 0.8358 (t80) REVERT: C 1132 TRP cc_start: 0.8718 (t60) cc_final: 0.8159 (t60) REVERT: C 1133 LYS cc_start: 0.9433 (ttmt) cc_final: 0.9133 (tppt) REVERT: C 1144 VAL cc_start: 0.8394 (p) cc_final: 0.8003 (m) REVERT: C 1165 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 1214 LEU cc_start: 0.9262 (mt) cc_final: 0.9057 (mt) REVERT: C 1314 MET cc_start: 0.9207 (mtm) cc_final: 0.8960 (ptp) REVERT: C 1323 TYR cc_start: 0.8278 (t80) cc_final: 0.7862 (t80) REVERT: D 32 MET cc_start: 0.8964 (tpt) cc_final: 0.8664 (tpp) REVERT: D 121 MET cc_start: 0.8578 (tpp) cc_final: 0.8122 (tpt) REVERT: D 291 SER cc_start: 0.8991 (p) cc_final: 0.8623 (t) REVERT: D 310 GLN cc_start: 0.8778 (mp10) cc_final: 0.8494 (mp10) REVERT: D 356 ASP cc_start: 0.9234 (m-30) cc_final: 0.8965 (t0) REVERT: D 360 ARG cc_start: 0.8633 (mpt180) cc_final: 0.8290 (mpt-90) REVERT: D 363 ILE cc_start: 0.9224 (tp) cc_final: 0.8995 (tp) REVERT: D 389 ASN cc_start: 0.8823 (m-40) cc_final: 0.8601 (m-40) REVERT: D 415 MET cc_start: 0.6716 (pmm) cc_final: 0.4869 (pmm) REVERT: D 418 SER cc_start: 0.9032 (t) cc_final: 0.8767 (t) REVERT: D 461 LEU cc_start: 0.9168 (mm) cc_final: 0.8944 (mm) REVERT: D 479 HIS cc_start: 0.9237 (m-70) cc_final: 0.8970 (m90) REVERT: D 496 TYR cc_start: 0.7884 (m-80) cc_final: 0.7610 (m-80) REVERT: D 543 TYR cc_start: 0.8604 (p90) cc_final: 0.8015 (p90) REVERT: D 545 VAL cc_start: 0.8679 (t) cc_final: 0.7876 (t) REVERT: D 552 ILE cc_start: 0.9349 (pt) cc_final: 0.9035 (pt) REVERT: D 572 PHE cc_start: 0.8493 (p90) cc_final: 0.8115 (p90) REVERT: D 650 ILE cc_start: 0.6901 (mm) cc_final: 0.6680 (mm) REVERT: D 669 PHE cc_start: 0.8636 (m-80) cc_final: 0.8343 (m-80) REVERT: D 798 MET cc_start: 0.8248 (mpp) cc_final: 0.7960 (mpp) REVERT: D 877 LEU cc_start: 0.8901 (mt) cc_final: 0.8447 (tt) REVERT: D 968 MET cc_start: 0.8286 (tpt) cc_final: 0.8033 (tpt) REVERT: D 985 TYR cc_start: 0.9121 (m-80) cc_final: 0.8772 (m-80) REVERT: D 1067 LEU cc_start: 0.8795 (mt) cc_final: 0.8588 (mt) REVERT: D 1165 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8869 (tt0) REVERT: D 1205 GLU cc_start: 0.8381 (pt0) cc_final: 0.8060 (tt0) REVERT: D 1330 TYR cc_start: 0.9011 (p90) cc_final: 0.8732 (p90) REVERT: D 1331 ASN cc_start: 0.6155 (m110) cc_final: 0.4232 (m110) outliers start: 3 outliers final: 0 residues processed: 837 average time/residue: 0.2266 time to fit residues: 314.6022 Evaluate side-chains 685 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 53 optimal weight: 0.9990 chunk 377 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 287 optimal weight: 0.7980 chunk 392 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 582 HIS A 584 HIS A 917 ASN ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 HIS B 441 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B1017 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 441 HIS C 582 HIS C 584 HIS C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS D 523 HIS ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 GLN D1017 ASN D1036 GLN D1242 GLN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.090720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069210 restraints weight = 166879.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.071941 restraints weight = 116642.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.074098 restraints weight = 87921.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.075809 restraints weight = 69363.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.077162 restraints weight = 56915.495| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41259 Z= 0.132 Angle : 0.754 12.002 56144 Z= 0.369 Chirality : 0.049 0.335 6471 Planarity : 0.005 0.072 7166 Dihedral : 5.605 39.435 5444 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.60 % Favored : 90.36 % Rotamer: Outliers : 0.11 % Allowed : 1.26 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.66 (0.11), residues: 5084 helix: 0.24 (0.17), residues: 882 sheet: -1.36 (0.12), residues: 1835 loop : -2.91 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 787 TYR 0.025 0.001 TYR D1152 PHE 0.051 0.002 PHE C1049 TRP 0.043 0.002 TRP B 739 HIS 0.007 0.001 HIS B 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (41179) covalent geometry : angle 0.74008 / 0.37 (55948) SS BOND : bond 0.00648 / 0.41 ( 44) SS BOND : angle 2.04878 / 1.34 ( 88) hydrogen bonds : bond 0.04699 / 3.12 ( 536) hydrogen bonds : angle 4.80445 / 3.32 ( 1608) link_BETA1-4 : bond 0.00738 / 0.32 ( 8) link_BETA1-4 : angle 2.14317 / 1.33 ( 24) link_NAG-ASN : bond 0.00698 / 0.45 ( 28) link_NAG-ASN : angle 3.02303 / 2.03 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 853 time to evaluate : 1.580 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 32 MET cc_start: 0.9423 (ttt) cc_final: 0.9058 (ttt) REVERT: A 50 LEU cc_start: 0.9338 (tt) cc_final: 0.8282 (mm) REVERT: A 121 MET cc_start: 0.9047 (mmt) cc_final: 0.8587 (mpp) REVERT: A 131 VAL cc_start: 0.9288 (t) cc_final: 0.9008 (t) REVERT: A 151 MET cc_start: 0.4400 (ttm) cc_final: 0.3736 (tpp) REVERT: A 183 LEU cc_start: 0.8376 (tp) cc_final: 0.8171 (tp) REVERT: A 209 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8356 (mmtm) REVERT: A 251 CYS cc_start: 0.8345 (m) cc_final: 0.7946 (t) REVERT: A 271 LYS cc_start: 0.7651 (mptt) cc_final: 0.7190 (mptt) REVERT: A 290 PHE cc_start: 0.9400 (m-80) cc_final: 0.9013 (m-80) REVERT: A 373 ASP cc_start: 0.8074 (t0) cc_final: 0.7623 (t0) REVERT: A 415 MET cc_start: 0.5378 (ppp) cc_final: 0.5074 (ppp) REVERT: A 425 TYR cc_start: 0.5067 (t80) cc_final: 0.4784 (t80) REVERT: A 428 ARG cc_start: 0.5634 (mpt180) cc_final: 0.5043 (mtt180) REVERT: A 462 GLU cc_start: 0.7623 (pt0) cc_final: 0.7322 (pm20) REVERT: A 523 HIS cc_start: 0.9219 (m-70) cc_final: 0.8957 (m-70) REVERT: A 564 LEU cc_start: 0.9403 (mm) cc_final: 0.9025 (tp) REVERT: A 582 HIS cc_start: 0.9205 (t-170) cc_final: 0.8798 (p-80) REVERT: A 626 ASP cc_start: 0.8958 (p0) cc_final: 0.8207 (t0) REVERT: A 627 LEU cc_start: 0.9042 (mm) cc_final: 0.8707 (mp) REVERT: A 666 MET cc_start: 0.9013 (ttm) cc_final: 0.8471 (ptp) REVERT: A 671 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9280 (mm-30) REVERT: A 800 TYR cc_start: 0.8955 (p90) cc_final: 0.8700 (p90) REVERT: A 913 GLU cc_start: 0.9444 (pm20) cc_final: 0.8607 (pp20) REVERT: A 975 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8406 (tp-100) REVERT: A 983 ASN cc_start: 0.9428 (m-40) cc_final: 0.9073 (m110) REVERT: A 988 ASP cc_start: 0.8726 (m-30) cc_final: 0.8505 (m-30) REVERT: A 1020 HIS cc_start: 0.8879 (t-90) cc_final: 0.8551 (t-90) REVERT: A 1028 PHE cc_start: 0.8470 (m-10) cc_final: 0.8070 (t80) REVERT: A 1057 PHE cc_start: 0.8729 (t80) cc_final: 0.8342 (t80) REVERT: A 1076 ASP cc_start: 0.8878 (p0) cc_final: 0.8350 (m-30) REVERT: A 1132 TRP cc_start: 0.8589 (t60) cc_final: 0.8160 (t60) REVERT: A 1144 VAL cc_start: 0.8382 (p) cc_final: 0.7987 (m) REVERT: A 1154 PHE cc_start: 0.9173 (m-80) cc_final: 0.8014 (m-80) REVERT: A 1165 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 1323 TYR cc_start: 0.8052 (t80) cc_final: 0.7693 (t80) REVERT: B 121 MET cc_start: 0.8688 (tpp) cc_final: 0.8243 (tpt) REVERT: B 134 ASP cc_start: 0.9172 (t70) cc_final: 0.8497 (t70) REVERT: B 151 MET cc_start: 0.4787 (ttt) cc_final: 0.3914 (mtm) REVERT: B 216 GLU cc_start: 0.9041 (pp20) cc_final: 0.8729 (pp20) REVERT: B 310 GLN cc_start: 0.8745 (mp10) cc_final: 0.8393 (mp10) REVERT: B 354 LYS cc_start: 0.8518 (tttp) cc_final: 0.7708 (mttt) REVERT: B 356 ASP cc_start: 0.9246 (m-30) cc_final: 0.8907 (t0) REVERT: B 360 ARG cc_start: 0.8571 (mpt180) cc_final: 0.8211 (mpt-90) REVERT: B 363 ILE cc_start: 0.9268 (tp) cc_final: 0.9025 (tp) REVERT: B 389 ASN cc_start: 0.8715 (m-40) cc_final: 0.8437 (m-40) REVERT: B 394 TYR cc_start: 0.7903 (t80) cc_final: 0.7579 (t80) REVERT: B 415 MET cc_start: 0.6761 (pmm) cc_final: 0.5001 (pmm) REVERT: B 418 SER cc_start: 0.8939 (t) cc_final: 0.8627 (t) REVERT: B 422 ARG cc_start: 0.8977 (mtt90) cc_final: 0.8410 (mtm-85) REVERT: B 461 LEU cc_start: 0.9174 (mm) cc_final: 0.8872 (mm) REVERT: B 479 HIS cc_start: 0.8922 (m-70) cc_final: 0.8603 (m90) REVERT: B 521 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7854 (mmtp) REVERT: B 539 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7018 (ttt180) REVERT: B 542 ILE cc_start: 0.9531 (mp) cc_final: 0.9245 (tp) REVERT: B 552 ILE cc_start: 0.9305 (pt) cc_final: 0.8821 (pt) REVERT: B 569 ASP cc_start: 0.9134 (t70) cc_final: 0.8922 (t70) REVERT: B 786 LEU cc_start: 0.9142 (mp) cc_final: 0.8915 (mp) REVERT: B 877 LEU cc_start: 0.9003 (mt) cc_final: 0.8593 (tt) REVERT: B 985 TYR cc_start: 0.9130 (m-80) cc_final: 0.8811 (m-80) REVERT: B 1057 PHE cc_start: 0.9036 (t80) cc_final: 0.8774 (t80) REVERT: B 1165 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8893 (tt0) REVERT: B 1205 GLU cc_start: 0.8379 (pt0) cc_final: 0.8131 (tt0) REVERT: B 1330 TYR cc_start: 0.9031 (p90) cc_final: 0.8643 (p90) REVERT: B 1331 ASN cc_start: 0.6289 (m110) cc_final: 0.4487 (m110) REVERT: C 32 MET cc_start: 0.9441 (ttt) cc_final: 0.9113 (ttt) REVERT: C 50 LEU cc_start: 0.9360 (tt) cc_final: 0.8334 (mm) REVERT: C 121 MET cc_start: 0.9095 (mmt) cc_final: 0.8612 (mpp) REVERT: C 131 VAL cc_start: 0.9270 (t) cc_final: 0.8986 (t) REVERT: C 151 MET cc_start: 0.4413 (ttm) cc_final: 0.3738 (tpp) REVERT: C 209 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8350 (mmtm) REVERT: C 271 LYS cc_start: 0.7746 (mptt) cc_final: 0.7488 (mmtt) REVERT: C 290 PHE cc_start: 0.9399 (m-80) cc_final: 0.9041 (m-80) REVERT: C 309 PHE cc_start: 0.8945 (m-80) cc_final: 0.8596 (m-80) REVERT: C 373 ASP cc_start: 0.8082 (t0) cc_final: 0.7671 (t0) REVERT: C 415 MET cc_start: 0.5216 (ppp) cc_final: 0.4908 (ppp) REVERT: C 425 TYR cc_start: 0.5028 (t80) cc_final: 0.4777 (t80) REVERT: C 428 ARG cc_start: 0.5592 (mpt180) cc_final: 0.4962 (mtt180) REVERT: C 462 GLU cc_start: 0.7651 (pt0) cc_final: 0.7352 (pm20) REVERT: C 523 HIS cc_start: 0.9215 (m-70) cc_final: 0.8955 (m-70) REVERT: C 542 ILE cc_start: 0.9345 (mp) cc_final: 0.9099 (tp) REVERT: C 564 LEU cc_start: 0.9397 (mm) cc_final: 0.9023 (tp) REVERT: C 582 HIS cc_start: 0.9220 (t-170) cc_final: 0.8812 (p-80) REVERT: C 626 ASP cc_start: 0.8912 (p0) cc_final: 0.8485 (t0) REVERT: C 628 THR cc_start: 0.8873 (p) cc_final: 0.8656 (p) REVERT: C 666 MET cc_start: 0.8967 (ttm) cc_final: 0.8601 (ptm) REVERT: C 669 PHE cc_start: 0.8404 (m-10) cc_final: 0.8128 (m-10) REVERT: C 800 TYR cc_start: 0.8849 (p90) cc_final: 0.8617 (p90) REVERT: C 975 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8429 (tp-100) REVERT: C 977 MET cc_start: 0.9317 (mmm) cc_final: 0.9062 (mmm) REVERT: C 983 ASN cc_start: 0.9399 (m-40) cc_final: 0.8941 (m110) REVERT: C 1020 HIS cc_start: 0.8856 (t-90) cc_final: 0.8521 (t-90) REVERT: C 1028 PHE cc_start: 0.8458 (m-10) cc_final: 0.8058 (t80) REVERT: C 1057 PHE cc_start: 0.8808 (t80) cc_final: 0.8392 (t80) REVERT: C 1144 VAL cc_start: 0.8399 (p) cc_final: 0.7985 (m) REVERT: C 1154 PHE cc_start: 0.9159 (m-80) cc_final: 0.8022 (m-80) REVERT: C 1165 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 1214 LEU cc_start: 0.9246 (mt) cc_final: 0.9036 (mt) REVERT: D 121 MET cc_start: 0.8689 (tpp) cc_final: 0.8239 (tpt) REVERT: D 151 MET cc_start: 0.4800 (ttt) cc_final: 0.4425 (mpp) REVERT: D 216 GLU cc_start: 0.9108 (pp20) cc_final: 0.8792 (pp20) REVERT: D 310 GLN cc_start: 0.8739 (mp10) cc_final: 0.8386 (mp10) REVERT: D 354 LYS cc_start: 0.8483 (tptm) cc_final: 0.7744 (mmtt) REVERT: D 356 ASP cc_start: 0.9307 (m-30) cc_final: 0.8905 (t0) REVERT: D 360 ARG cc_start: 0.8470 (mpt180) cc_final: 0.8058 (mtt180) REVERT: D 363 ILE cc_start: 0.9274 (tp) cc_final: 0.8974 (tp) REVERT: D 389 ASN cc_start: 0.8670 (m-40) cc_final: 0.8381 (m-40) REVERT: D 394 TYR cc_start: 0.7828 (t80) cc_final: 0.7430 (t80) REVERT: D 415 MET cc_start: 0.6734 (pmm) cc_final: 0.4980 (pmm) REVERT: D 418 SER cc_start: 0.8942 (t) cc_final: 0.8648 (t) REVERT: D 422 ARG cc_start: 0.8989 (mtt90) cc_final: 0.8388 (mtm-85) REVERT: D 479 HIS cc_start: 0.8912 (m-70) cc_final: 0.8592 (m90) REVERT: D 521 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7847 (mmtp) REVERT: D 542 ILE cc_start: 0.9541 (mp) cc_final: 0.9260 (tp) REVERT: D 543 TYR cc_start: 0.8620 (p90) cc_final: 0.8322 (p90) REVERT: D 550 ASP cc_start: 0.9164 (m-30) cc_final: 0.8921 (t70) REVERT: D 552 ILE cc_start: 0.9327 (pt) cc_final: 0.8805 (pt) REVERT: D 572 PHE cc_start: 0.8478 (p90) cc_final: 0.8222 (p90) REVERT: D 650 ILE cc_start: 0.6919 (mm) cc_final: 0.6715 (mm) REVERT: D 688 MET cc_start: 0.8240 (ppp) cc_final: 0.8032 (ppp) REVERT: D 798 MET cc_start: 0.8216 (mpp) cc_final: 0.7820 (mpp) REVERT: D 877 LEU cc_start: 0.9004 (mt) cc_final: 0.8594 (tt) REVERT: D 967 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8757 (mp10) REVERT: D 985 TYR cc_start: 0.9155 (m-80) cc_final: 0.8778 (m-80) REVERT: D 1057 PHE cc_start: 0.9049 (t80) cc_final: 0.8773 (t80) REVERT: D 1067 LEU cc_start: 0.8783 (mt) cc_final: 0.8579 (mt) REVERT: D 1165 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8892 (tt0) REVERT: D 1328 LEU cc_start: 0.9510 (tp) cc_final: 0.8861 (tp) REVERT: D 1330 TYR cc_start: 0.8999 (p90) cc_final: 0.8616 (p90) REVERT: D 1331 ASN cc_start: 0.6152 (m110) cc_final: 0.4436 (m110) outliers start: 5 outliers final: 0 residues processed: 858 average time/residue: 0.2286 time to fit residues: 326.4397 Evaluate side-chains 702 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 701 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 166 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 501 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 504 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 372 optimal weight: 0.0050 chunk 212 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 917 ASN A1072 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 441 HIS C 917 ASN C 994 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1036 GLN D1062 HIS D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.083647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063375 restraints weight = 180935.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065809 restraints weight = 125883.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067728 restraints weight = 94632.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069210 restraints weight = 74889.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070428 restraints weight = 61873.407| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 41259 Z= 0.256 Angle : 0.869 14.141 56144 Z= 0.438 Chirality : 0.052 0.431 6471 Planarity : 0.006 0.065 7166 Dihedral : 6.105 36.606 5444 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.09 % Favored : 88.83 % Rotamer: Outliers : 0.07 % Allowed : 1.42 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.11), residues: 5084 helix: -0.22 (0.16), residues: 898 sheet: -1.81 (0.12), residues: 1775 loop : -2.93 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1053 TYR 0.028 0.002 TYR B1152 PHE 0.042 0.003 PHE C1049 TRP 0.042 0.004 TRP D1132 HIS 0.010 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.26 (41179) covalent geometry : angle 0.85394 / 0.43 (55948) SS BOND : bond 0.00559 / 0.34 ( 44) SS BOND : angle 2.12889 / 1.32 ( 88) hydrogen bonds : bond 0.05008 / 3.36 ( 536) hydrogen bonds : angle 5.18940 / 3.60 ( 1608) link_BETA1-4 : bond 0.00683 / 0.33 ( 8) link_BETA1-4 : angle 2.55302 / 1.63 ( 24) link_NAG-ASN : bond 0.00790 / 0.52 ( 28) link_NAG-ASN : angle 3.48058 / 2.13 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 821 time to evaluate : 1.585 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: 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: 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: 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: 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: 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: A 32 MET cc_start: 0.9474 (ttt) cc_final: 0.9029 (ttt) REVERT: A 38 LEU cc_start: 0.8146 (tt) cc_final: 0.7839 (tt) REVERT: A 121 MET cc_start: 0.9032 (mmt) cc_final: 0.8779 (mpp) REVERT: A 131 VAL cc_start: 0.9223 (t) cc_final: 0.8640 (t) REVERT: A 137 ILE cc_start: 0.8952 (tt) cc_final: 0.8737 (tt) REVERT: A 146 PHE cc_start: 0.9274 (p90) cc_final: 0.9048 (p90) REVERT: A 251 CYS cc_start: 0.8471 (m) cc_final: 0.8146 (t) REVERT: A 271 LYS cc_start: 0.8011 (mptt) cc_final: 0.7595 (mptt) REVERT: A 290 PHE cc_start: 0.9475 (m-80) cc_final: 0.9131 (m-80) REVERT: A 309 PHE cc_start: 0.9090 (m-80) cc_final: 0.8870 (m-80) REVERT: A 415 MET cc_start: 0.5635 (ppp) cc_final: 0.5273 (ppp) REVERT: A 425 TYR cc_start: 0.5119 (t80) cc_final: 0.4794 (t80) REVERT: A 428 ARG cc_start: 0.6072 (mpt180) cc_final: 0.5375 (mtt180) REVERT: A 464 MET cc_start: 0.9571 (tpt) cc_final: 0.9370 (tpt) REVERT: A 491 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9116 (mmmt) REVERT: A 523 HIS cc_start: 0.9286 (m-70) cc_final: 0.8986 (m-70) REVERT: A 564 LEU cc_start: 0.9455 (mm) cc_final: 0.9159 (tp) REVERT: A 582 HIS cc_start: 0.9287 (t-170) cc_final: 0.8918 (p-80) REVERT: A 626 ASP cc_start: 0.9099 (p0) cc_final: 0.8497 (t0) REVERT: A 627 LEU cc_start: 0.9183 (mm) cc_final: 0.8939 (mp) REVERT: A 666 MET cc_start: 0.9142 (ttm) cc_final: 0.8859 (ptm) REVERT: A 669 PHE cc_start: 0.8586 (m-10) cc_final: 0.8321 (m-10) REVERT: A 800 TYR cc_start: 0.9011 (p90) cc_final: 0.8625 (p90) REVERT: A 931 LEU cc_start: 0.8932 (tp) cc_final: 0.8385 (tt) REVERT: A 933 LEU cc_start: 0.9239 (mt) cc_final: 0.8894 (mt) REVERT: A 975 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8534 (tp-100) REVERT: A 988 ASP cc_start: 0.8960 (m-30) cc_final: 0.8582 (m-30) REVERT: A 1020 HIS cc_start: 0.8996 (t-90) cc_final: 0.8707 (t-90) REVERT: A 1057 PHE cc_start: 0.8651 (t80) cc_final: 0.8312 (t80) REVERT: A 1076 ASP cc_start: 0.8778 (p0) cc_final: 0.8562 (m-30) REVERT: A 1132 TRP cc_start: 0.8653 (t60) cc_final: 0.7787 (t60) REVERT: A 1133 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9224 (tppt) REVERT: A 1144 VAL cc_start: 0.8551 (p) cc_final: 0.8115 (m) REVERT: A 1154 PHE cc_start: 0.9286 (m-80) cc_final: 0.8314 (m-80) REVERT: A 1165 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 1323 TYR cc_start: 0.8395 (t80) cc_final: 0.8007 (t80) REVERT: B 54 LEU cc_start: 0.7818 (tp) cc_final: 0.7586 (tp) REVERT: B 121 MET cc_start: 0.8703 (tpp) cc_final: 0.8316 (tpt) REVERT: B 134 ASP cc_start: 0.9211 (t70) cc_final: 0.8569 (t70) REVERT: B 360 ARG cc_start: 0.8609 (mpt180) cc_final: 0.8166 (mpt-90) REVERT: B 363 ILE cc_start: 0.9299 (tp) cc_final: 0.9080 (tp) REVERT: B 389 ASN cc_start: 0.9134 (m-40) cc_final: 0.8931 (m-40) REVERT: B 394 TYR cc_start: 0.8070 (t80) cc_final: 0.7721 (t80) REVERT: B 415 MET cc_start: 0.7196 (pmm) cc_final: 0.6300 (pmm) REVERT: B 418 SER cc_start: 0.9289 (t) cc_final: 0.9061 (t) REVERT: B 421 VAL cc_start: 0.9631 (t) cc_final: 0.9397 (t) REVERT: B 422 ARG cc_start: 0.9129 (mtt90) cc_final: 0.8449 (mtm-85) REVERT: B 521 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7999 (mmtp) REVERT: B 539 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7133 (ttt180) REVERT: B 550 ASP cc_start: 0.9323 (t0) cc_final: 0.9029 (t0) REVERT: B 552 ILE cc_start: 0.9484 (pt) cc_final: 0.9107 (pt) REVERT: B 559 ASP cc_start: 0.8324 (t70) cc_final: 0.8122 (t70) REVERT: B 798 MET cc_start: 0.8279 (mpp) cc_final: 0.7979 (mpp) REVERT: B 870 PHE cc_start: 0.9388 (t80) cc_final: 0.9150 (t80) REVERT: B 877 LEU cc_start: 0.8949 (mt) cc_final: 0.8486 (tt) REVERT: B 985 TYR cc_start: 0.9157 (m-80) cc_final: 0.8881 (m-80) REVERT: B 1044 PHE cc_start: 0.9397 (t80) cc_final: 0.9151 (t80) REVERT: B 1057 PHE cc_start: 0.9031 (t80) cc_final: 0.8817 (t80) REVERT: B 1165 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9023 (tt0) REVERT: B 1205 GLU cc_start: 0.8526 (pt0) cc_final: 0.8223 (tt0) REVERT: B 1241 GLN cc_start: 0.7599 (mp-120) cc_final: 0.7328 (mp10) REVERT: B 1316 VAL cc_start: 0.8403 (t) cc_final: 0.8096 (p) REVERT: B 1330 TYR cc_start: 0.9094 (p90) cc_final: 0.8825 (p90) REVERT: C 32 MET cc_start: 0.9492 (ttt) cc_final: 0.9066 (ttt) REVERT: C 38 LEU cc_start: 0.8130 (tt) cc_final: 0.7803 (tt) REVERT: C 121 MET cc_start: 0.9036 (mmt) cc_final: 0.8761 (mpp) REVERT: C 131 VAL cc_start: 0.9208 (t) cc_final: 0.8642 (t) REVERT: C 137 ILE cc_start: 0.8962 (tt) cc_final: 0.8746 (tt) REVERT: C 146 PHE cc_start: 0.9265 (p90) cc_final: 0.9054 (p90) REVERT: C 251 CYS cc_start: 0.8441 (m) cc_final: 0.8144 (t) REVERT: C 290 PHE cc_start: 0.9484 (m-80) cc_final: 0.9148 (m-80) REVERT: C 309 PHE cc_start: 0.9082 (m-80) cc_final: 0.8651 (m-80) REVERT: C 415 MET cc_start: 0.5700 (ppp) cc_final: 0.5365 (ppp) REVERT: C 425 TYR cc_start: 0.5148 (t80) cc_final: 0.4794 (t80) REVERT: C 428 ARG cc_start: 0.6044 (mpt180) cc_final: 0.5323 (mtt180) REVERT: C 491 LYS cc_start: 0.9383 (mmpt) cc_final: 0.9125 (mmmt) REVERT: C 523 HIS cc_start: 0.9283 (m-70) cc_final: 0.8984 (m-70) REVERT: C 564 LEU cc_start: 0.9452 (mm) cc_final: 0.9163 (tp) REVERT: C 582 HIS cc_start: 0.9284 (t-170) cc_final: 0.8915 (p-80) REVERT: C 626 ASP cc_start: 0.9037 (p0) cc_final: 0.8492 (t0) REVERT: C 666 MET cc_start: 0.9071 (ttm) cc_final: 0.8753 (ptm) REVERT: C 669 PHE cc_start: 0.8656 (m-10) cc_final: 0.8404 (m-80) REVERT: C 913 GLU cc_start: 0.9470 (pm20) cc_final: 0.9089 (pm20) REVERT: C 931 LEU cc_start: 0.8911 (tp) cc_final: 0.8650 (tt) REVERT: C 933 LEU cc_start: 0.9215 (mt) cc_final: 0.9004 (mt) REVERT: C 975 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8550 (tp-100) REVERT: C 1020 HIS cc_start: 0.8959 (t-90) cc_final: 0.8661 (t-90) REVERT: C 1028 PHE cc_start: 0.8549 (m-10) cc_final: 0.8165 (t80) REVERT: C 1057 PHE cc_start: 0.8747 (t80) cc_final: 0.8416 (t80) REVERT: C 1144 VAL cc_start: 0.8515 (p) cc_final: 0.8057 (m) REVERT: C 1154 PHE cc_start: 0.9282 (m-80) cc_final: 0.8284 (m-80) REVERT: C 1165 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 1214 LEU cc_start: 0.9366 (mt) cc_final: 0.9148 (mt) REVERT: C 1323 TYR cc_start: 0.8132 (t80) cc_final: 0.6617 (t80) REVERT: C 1324 LEU cc_start: 0.8420 (mp) cc_final: 0.8121 (tt) REVERT: D 121 MET cc_start: 0.8695 (tpp) cc_final: 0.8309 (tpt) REVERT: D 151 MET cc_start: 0.5325 (ttt) cc_final: 0.3703 (mtm) REVERT: D 354 LYS cc_start: 0.8756 (tptm) cc_final: 0.7955 (tptm) REVERT: D 360 ARG cc_start: 0.8575 (mpt180) cc_final: 0.8296 (mpt-90) REVERT: D 363 ILE cc_start: 0.9306 (tp) cc_final: 0.8949 (tp) REVERT: D 389 ASN cc_start: 0.9114 (m-40) cc_final: 0.8860 (m-40) REVERT: D 415 MET cc_start: 0.7171 (pmm) cc_final: 0.6284 (pmm) REVERT: D 418 SER cc_start: 0.9279 (t) cc_final: 0.9030 (t) REVERT: D 421 VAL cc_start: 0.9636 (t) cc_final: 0.9403 (t) REVERT: D 422 ARG cc_start: 0.9144 (mtt90) cc_final: 0.8441 (mtm-85) REVERT: D 521 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7997 (mmtp) REVERT: D 539 ARG cc_start: 0.8525 (mtt180) cc_final: 0.7100 (ttt180) REVERT: D 550 ASP cc_start: 0.9230 (m-30) cc_final: 0.8982 (m-30) REVERT: D 552 ILE cc_start: 0.9438 (pt) cc_final: 0.9029 (pt) REVERT: D 559 ASP cc_start: 0.8282 (t70) cc_final: 0.8072 (t70) REVERT: D 586 ARG cc_start: 0.9026 (ttt90) cc_final: 0.8375 (tpp80) REVERT: D 587 VAL cc_start: 0.9434 (t) cc_final: 0.8991 (t) REVERT: D 770 PHE cc_start: 0.8877 (t80) cc_final: 0.8640 (t80) REVERT: D 798 MET cc_start: 0.8148 (mpp) cc_final: 0.7942 (mpp) REVERT: D 870 PHE cc_start: 0.9424 (t80) cc_final: 0.9157 (t80) REVERT: D 877 LEU cc_start: 0.8965 (mt) cc_final: 0.8523 (tt) REVERT: D 985 TYR cc_start: 0.9169 (m-80) cc_final: 0.8878 (m-80) REVERT: D 1044 PHE cc_start: 0.9395 (t80) cc_final: 0.9124 (t80) REVERT: D 1057 PHE cc_start: 0.9065 (t80) cc_final: 0.8845 (t80) REVERT: D 1067 LEU cc_start: 0.8876 (mt) cc_final: 0.8661 (mt) REVERT: D 1165 GLU cc_start: 0.9268 (mm-30) cc_final: 0.9003 (tt0) REVERT: D 1241 GLN cc_start: 0.7603 (mp-120) cc_final: 0.7318 (mp10) REVERT: D 1316 VAL cc_start: 0.8385 (t) cc_final: 0.8077 (p) REVERT: D 1328 LEU cc_start: 0.9489 (tp) cc_final: 0.8858 (tp) REVERT: D 1330 TYR cc_start: 0.9147 (p90) cc_final: 0.8745 (p90) outliers start: 3 outliers final: 0 residues processed: 824 average time/residue: 0.2340 time to fit residues: 319.9433 Evaluate side-chains 673 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 416 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 483 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 917 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 321 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 GLN B1017 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 523 HIS C 917 ASN C 994 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 816 ASN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1035 ASN D1062 HIS D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.085723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065108 restraints weight = 173513.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067604 restraints weight = 121137.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.069568 restraints weight = 91237.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.071128 restraints weight = 72484.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.072355 restraints weight = 59552.258| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 41259 Z= 0.166 Angle : 0.800 12.267 56144 Z= 0.398 Chirality : 0.050 0.334 6471 Planarity : 0.006 0.082 7166 Dihedral : 5.934 36.106 5444 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.13 % Favored : 89.79 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.95 (0.11), residues: 5084 helix: 0.04 (0.17), residues: 892 sheet: -1.77 (0.12), residues: 1823 loop : -2.92 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 732 TYR 0.026 0.002 TYR B 734 PHE 0.049 0.002 PHE C1049 TRP 0.047 0.003 TRP B 741 HIS 0.006 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (41179) covalent geometry : angle 0.78415 / 0.39 (55948) SS BOND : bond 0.00659 / 0.35 ( 44) SS BOND : angle 2.43180 / 1.50 ( 88) hydrogen bonds : bond 0.04809 / 3.25 ( 536) hydrogen bonds : angle 4.96852 / 3.44 ( 1608) link_BETA1-4 : bond 0.00851 / 0.51 ( 8) link_BETA1-4 : angle 2.30718 / 1.39 ( 24) link_NAG-ASN : bond 0.00667 / 0.43 ( 28) link_NAG-ASN : angle 3.18871 / 2.03 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 822 time to evaluate : 1.362 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 121 MET cc_start: 0.9077 (mmt) cc_final: 0.8710 (mpp) REVERT: A 131 VAL cc_start: 0.9284 (t) cc_final: 0.8640 (t) REVERT: A 137 ILE cc_start: 0.8746 (tt) cc_final: 0.8498 (tt) REVERT: A 146 PHE cc_start: 0.9264 (p90) cc_final: 0.9051 (p90) REVERT: A 251 CYS cc_start: 0.8394 (m) cc_final: 0.8047 (t) REVERT: A 271 LYS cc_start: 0.7905 (mptt) cc_final: 0.7593 (mptt) REVERT: A 290 PHE cc_start: 0.9466 (m-80) cc_final: 0.9112 (m-80) REVERT: A 301 TYR cc_start: 0.6962 (t80) cc_final: 0.6687 (t80) REVERT: A 312 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9132 (mmtt) REVERT: A 373 ASP cc_start: 0.8276 (t0) cc_final: 0.7999 (t0) REVERT: A 425 TYR cc_start: 0.5154 (t80) cc_final: 0.4873 (t80) REVERT: A 428 ARG cc_start: 0.5991 (mpt180) cc_final: 0.5327 (mtt180) REVERT: A 462 GLU cc_start: 0.7672 (pt0) cc_final: 0.7438 (pm20) REVERT: A 464 MET cc_start: 0.9499 (tpt) cc_final: 0.9284 (tpp) REVERT: A 500 MET cc_start: 0.4779 (mmp) cc_final: 0.3232 (mtt) REVERT: A 523 HIS cc_start: 0.9309 (m-70) cc_final: 0.9025 (m-70) REVERT: A 582 HIS cc_start: 0.9255 (t-170) cc_final: 0.8894 (p-80) REVERT: A 626 ASP cc_start: 0.9080 (p0) cc_final: 0.8408 (t0) REVERT: A 627 LEU cc_start: 0.9167 (mm) cc_final: 0.8932 (mp) REVERT: A 666 MET cc_start: 0.9098 (ttm) cc_final: 0.8748 (ptm) REVERT: A 669 PHE cc_start: 0.8589 (m-10) cc_final: 0.8371 (m-80) REVERT: A 800 TYR cc_start: 0.8986 (p90) cc_final: 0.8570 (p90) REVERT: A 931 LEU cc_start: 0.8926 (tp) cc_final: 0.8334 (tt) REVERT: A 933 LEU cc_start: 0.9251 (mt) cc_final: 0.8909 (mt) REVERT: A 965 LEU cc_start: 0.9259 (tt) cc_final: 0.9045 (tt) REVERT: A 975 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8425 (tp-100) REVERT: A 983 ASN cc_start: 0.9402 (m-40) cc_final: 0.9131 (m110) REVERT: A 988 ASP cc_start: 0.8985 (m-30) cc_final: 0.8602 (m-30) REVERT: A 1020 HIS cc_start: 0.8927 (t-90) cc_final: 0.8599 (t-90) REVERT: A 1028 PHE cc_start: 0.8542 (m-80) cc_final: 0.8170 (t80) REVERT: A 1057 PHE cc_start: 0.8653 (t80) cc_final: 0.8373 (t80) REVERT: A 1076 ASP cc_start: 0.8727 (p0) cc_final: 0.8480 (m-30) REVERT: A 1132 TRP cc_start: 0.8582 (t60) cc_final: 0.7748 (t60) REVERT: A 1133 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9230 (tppt) REVERT: A 1144 VAL cc_start: 0.8485 (p) cc_final: 0.8019 (m) REVERT: A 1154 PHE cc_start: 0.9287 (m-80) cc_final: 0.8226 (m-80) REVERT: A 1165 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 1314 MET cc_start: 0.9185 (ptp) cc_final: 0.8970 (ptp) REVERT: A 1323 TYR cc_start: 0.8307 (t80) cc_final: 0.7309 (t80) REVERT: A 1324 LEU cc_start: 0.8283 (mp) cc_final: 0.8050 (tt) REVERT: B 121 MET cc_start: 0.8715 (tpp) cc_final: 0.8319 (tpt) REVERT: B 161 LEU cc_start: 0.9468 (tp) cc_final: 0.9182 (pt) REVERT: B 310 GLN cc_start: 0.8780 (mp10) cc_final: 0.8462 (mp10) REVERT: B 363 ILE cc_start: 0.9268 (tp) cc_final: 0.9066 (tp) REVERT: B 389 ASN cc_start: 0.8947 (m-40) cc_final: 0.8724 (m-40) REVERT: B 394 TYR cc_start: 0.8043 (t80) cc_final: 0.7738 (t80) REVERT: B 411 THR cc_start: 0.8741 (m) cc_final: 0.8467 (p) REVERT: B 415 MET cc_start: 0.7152 (pmm) cc_final: 0.6284 (pmm) REVERT: B 418 SER cc_start: 0.9184 (t) cc_final: 0.8913 (t) REVERT: B 422 ARG cc_start: 0.9140 (mtt90) cc_final: 0.8431 (mtm-85) REVERT: B 479 HIS cc_start: 0.9059 (m90) cc_final: 0.8702 (m90) REVERT: B 521 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7799 (mmtm) REVERT: B 543 TYR cc_start: 0.8642 (p90) cc_final: 0.8375 (p90) REVERT: B 550 ASP cc_start: 0.9259 (t0) cc_final: 0.8984 (t0) REVERT: B 552 ILE cc_start: 0.9422 (pt) cc_final: 0.9005 (pt) REVERT: B 559 ASP cc_start: 0.8335 (t70) cc_final: 0.8111 (t70) REVERT: B 688 MET cc_start: 0.8123 (ppp) cc_final: 0.7751 (ppp) REVERT: B 870 PHE cc_start: 0.9333 (t80) cc_final: 0.9077 (t80) REVERT: B 877 LEU cc_start: 0.8999 (mt) cc_final: 0.8560 (tt) REVERT: B 968 MET cc_start: 0.8426 (tpt) cc_final: 0.8110 (tpt) REVERT: B 985 TYR cc_start: 0.9033 (m-80) cc_final: 0.8792 (m-80) REVERT: B 994 GLN cc_start: 0.9293 (tp40) cc_final: 0.9079 (tp-100) REVERT: B 1044 PHE cc_start: 0.9414 (t80) cc_final: 0.9181 (t80) REVERT: B 1057 PHE cc_start: 0.9069 (t80) cc_final: 0.8854 (t80) REVERT: B 1067 LEU cc_start: 0.8826 (mt) cc_final: 0.8597 (mt) REVERT: B 1165 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8968 (tt0) REVERT: B 1241 GLN cc_start: 0.7462 (mp-120) cc_final: 0.7172 (mp10) REVERT: B 1316 VAL cc_start: 0.8298 (t) cc_final: 0.7930 (p) REVERT: B 1328 LEU cc_start: 0.9404 (tp) cc_final: 0.8964 (tp) REVERT: B 1330 TYR cc_start: 0.8975 (p90) cc_final: 0.8497 (p90) REVERT: C 32 MET cc_start: 0.9483 (ttt) cc_final: 0.9064 (ttt) REVERT: C 121 MET cc_start: 0.9074 (mmt) cc_final: 0.8823 (mmp) REVERT: C 131 VAL cc_start: 0.9281 (t) cc_final: 0.8631 (t) REVERT: C 137 ILE cc_start: 0.8772 (tt) cc_final: 0.8540 (tt) REVERT: C 146 PHE cc_start: 0.9268 (p90) cc_final: 0.9060 (p90) REVERT: C 251 CYS cc_start: 0.8372 (m) cc_final: 0.8030 (t) REVERT: C 290 PHE cc_start: 0.9471 (m-80) cc_final: 0.9126 (m-80) REVERT: C 309 PHE cc_start: 0.8901 (m-80) cc_final: 0.8674 (m-80) REVERT: C 373 ASP cc_start: 0.8294 (t0) cc_final: 0.8041 (t0) REVERT: C 425 TYR cc_start: 0.5154 (t80) cc_final: 0.4878 (t80) REVERT: C 428 ARG cc_start: 0.5947 (mpt180) cc_final: 0.5270 (mtt180) REVERT: C 464 MET cc_start: 0.9440 (tpt) cc_final: 0.9231 (tpp) REVERT: C 500 MET cc_start: 0.4776 (mmp) cc_final: 0.3246 (mtt) REVERT: C 523 HIS cc_start: 0.9249 (m90) cc_final: 0.8993 (m-70) REVERT: C 542 ILE cc_start: 0.9316 (mp) cc_final: 0.9092 (tp) REVERT: C 582 HIS cc_start: 0.9260 (t-170) cc_final: 0.8895 (p-80) REVERT: C 626 ASP cc_start: 0.9005 (p0) cc_final: 0.8451 (t0) REVERT: C 666 MET cc_start: 0.9052 (ttm) cc_final: 0.8732 (ptp) REVERT: C 669 PHE cc_start: 0.8598 (m-10) cc_final: 0.8368 (m-10) REVERT: C 800 TYR cc_start: 0.8841 (p90) cc_final: 0.8630 (p90) REVERT: C 913 GLU cc_start: 0.9453 (pm20) cc_final: 0.9089 (pm20) REVERT: C 931 LEU cc_start: 0.9178 (tp) cc_final: 0.8860 (tp) REVERT: C 933 LEU cc_start: 0.9250 (mt) cc_final: 0.9037 (mt) REVERT: C 965 LEU cc_start: 0.9235 (tt) cc_final: 0.9018 (tt) REVERT: C 975 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8466 (tp-100) REVERT: C 983 ASN cc_start: 0.9324 (m-40) cc_final: 0.9037 (m110) REVERT: C 1020 HIS cc_start: 0.8916 (t-90) cc_final: 0.8583 (t-90) REVERT: C 1028 PHE cc_start: 0.8550 (m-10) cc_final: 0.8129 (t80) REVERT: C 1057 PHE cc_start: 0.8715 (t80) cc_final: 0.8370 (t80) REVERT: C 1132 TRP cc_start: 0.8585 (t60) cc_final: 0.8063 (t60) REVERT: C 1133 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9130 (tppt) REVERT: C 1144 VAL cc_start: 0.8503 (p) cc_final: 0.8040 (m) REVERT: C 1154 PHE cc_start: 0.9294 (m-80) cc_final: 0.8226 (m-80) REVERT: C 1165 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 1214 LEU cc_start: 0.9347 (mt) cc_final: 0.9135 (mt) REVERT: C 1323 TYR cc_start: 0.8035 (t80) cc_final: 0.6498 (t80) REVERT: D 121 MET cc_start: 0.8715 (tpp) cc_final: 0.8313 (tpt) REVERT: D 310 GLN cc_start: 0.8829 (mp10) cc_final: 0.8526 (mp10) REVERT: D 360 ARG cc_start: 0.8374 (mpt180) cc_final: 0.7935 (mtt-85) REVERT: D 389 ASN cc_start: 0.8924 (m-40) cc_final: 0.8648 (m-40) REVERT: D 411 THR cc_start: 0.8734 (m) cc_final: 0.8458 (p) REVERT: D 415 MET cc_start: 0.7131 (pmm) cc_final: 0.6270 (pmm) REVERT: D 418 SER cc_start: 0.9179 (t) cc_final: 0.8925 (t) REVERT: D 422 ARG cc_start: 0.9142 (mtt90) cc_final: 0.8420 (mtm-85) REVERT: D 479 HIS cc_start: 0.9038 (m90) cc_final: 0.8660 (m90) REVERT: D 521 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7877 (mmtp) REVERT: D 543 TYR cc_start: 0.8601 (p90) cc_final: 0.8299 (p90) REVERT: D 550 ASP cc_start: 0.9121 (m-30) cc_final: 0.8905 (t70) REVERT: D 552 ILE cc_start: 0.9406 (pt) cc_final: 0.8935 (pt) REVERT: D 559 ASP cc_start: 0.8332 (t70) cc_final: 0.8111 (t70) REVERT: D 650 ILE cc_start: 0.7031 (mm) cc_final: 0.6824 (mm) REVERT: D 798 MET cc_start: 0.8108 (mpp) cc_final: 0.7857 (mpp) REVERT: D 858 TRP cc_start: 0.7691 (m-90) cc_final: 0.7015 (m-90) REVERT: D 870 PHE cc_start: 0.9334 (t80) cc_final: 0.9070 (t80) REVERT: D 877 LEU cc_start: 0.9005 (mt) cc_final: 0.8557 (tt) REVERT: D 985 TYR cc_start: 0.9107 (m-80) cc_final: 0.8839 (m-80) REVERT: D 1044 PHE cc_start: 0.9417 (t80) cc_final: 0.9164 (t80) REVERT: D 1067 LEU cc_start: 0.8873 (mt) cc_final: 0.8659 (mt) REVERT: D 1165 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8952 (tt0) REVERT: D 1241 GLN cc_start: 0.7476 (mp-120) cc_final: 0.7206 (mp10) REVERT: D 1316 VAL cc_start: 0.8287 (t) cc_final: 0.7910 (p) outliers start: 2 outliers final: 0 residues processed: 824 average time/residue: 0.2421 time to fit residues: 329.8970 Evaluate side-chains 688 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 254 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 406 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 446 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 373 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 562 ASN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1331 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 562 ASN C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN D 994 GLN D1089 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1331 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062726 restraints weight = 181663.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065067 restraints weight = 126446.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.066910 restraints weight = 95253.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068355 restraints weight = 75380.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069518 restraints weight = 62250.131| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 41259 Z= 0.232 Angle : 0.851 13.451 56144 Z= 0.429 Chirality : 0.051 0.337 6471 Planarity : 0.006 0.114 7166 Dihedral : 6.187 34.102 5444 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.11 % Favored : 88.81 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.11), residues: 5084 helix: -0.23 (0.16), residues: 899 sheet: -2.05 (0.11), residues: 1823 loop : -2.93 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 732 TYR 0.027 0.002 TYR B1152 PHE 0.055 0.003 PHE B1126 TRP 0.065 0.005 TRP C1183 HIS 0.011 0.002 HIS D 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (41179) covalent geometry : angle 0.83621 / 0.43 (55948) SS BOND : bond 0.00668 / 0.36 ( 44) SS BOND : angle 2.40886 / 1.50 ( 88) hydrogen bonds : bond 0.04930 / 3.34 ( 536) hydrogen bonds : angle 5.27754 / 3.69 ( 1608) link_BETA1-4 : bond 0.00621 / 0.37 ( 8) link_BETA1-4 : angle 2.29442 / 1.34 ( 24) link_NAG-ASN : bond 0.00710 / 0.46 ( 28) link_NAG-ASN : angle 3.28169 / 2.09 ( 84) =============================================================================== Job complete usr+sys time: 8337.64 seconds wall clock time: 145 minutes 29.34 seconds (8729.34 seconds total)