Starting phenix.real_space_refine on Sat Mar 7 07:36:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7p_12752/03_2026/7o7p_12752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7p_12752/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7p_12752/03_2026/7o7p_12752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7p_12752/03_2026/7o7p_12752.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7p_12752/03_2026/7o7p_12752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7p_12752/03_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.02, per 1000 atoms: 0.25 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: 4.25 Conformation dependent library (CDL) restraints added in 1.9 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: 0.88 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: 5.35 Time building geometry restraints manager: 5.39 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 - 23.34: 23638 23.34 - 46.68: 1458 46.68 - 70.02: 233 70.02 - 93.35: 40 93.35 - 116.69: 3 Dihedral angle restraints: 25372 sinusoidal: 10526 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 25369 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.450 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.100 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 15.253 116.693 15682 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 covalent geometry : bond 0.00937 (41179) covalent geometry : angle 1.14909 (55948) SS BOND : bond 0.01096 ( 44) SS BOND : angle 3.38132 ( 88) hydrogen bonds : bond 0.09646 ( 536) hydrogen bonds : angle 5.52873 ( 1608) link_BETA1-4 : bond 0.00252 ( 8) link_BETA1-4 : angle 1.76007 ( 24) link_NAG-ASN : bond 0.01346 ( 28) link_NAG-ASN : angle 3.83837 ( 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 : 1.516 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: 0.2555 time to fit residues: 476.8123 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 : 1.551 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 132 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 441 HIS A 582 HIS A 691 GLN A 960 GLN A 976 ASN A1241 GLN ** A1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 303 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 ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN 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 424 ASN 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.096148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.073898 restraints weight = 168920.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.076661 restraints weight = 121717.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.078875 restraints weight = 93453.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.080639 restraints weight = 74655.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082100 restraints weight = 61613.300| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 41259 Z= 0.220 Angle : 0.896 14.578 56144 Z= 0.445 Chirality : 0.053 0.524 6471 Planarity : 0.006 0.082 7166 Dihedral : 8.740 85.177 6200 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.29 % Favored : 89.63 % Rotamer: Outliers : 0.61 % Allowed : 7.48 % Favored : 91.91 % 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: -3.76 (0.10), residues: 5084 helix: -0.63 (0.16), residues: 866 sheet: -2.27 (0.11), residues: 1857 loop : -3.42 (0.11), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 945 TYR 0.026 0.002 TYR D 256 PHE 0.028 0.002 PHE D 114 TRP 0.034 0.002 TRP D1132 HIS 0.008 0.002 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00467 (41179) covalent geometry : angle 0.87400 (55948) SS BOND : bond 0.00430 ( 44) SS BOND : angle 2.37334 ( 88) hydrogen bonds : bond 0.05346 ( 536) hydrogen bonds : angle 5.14949 ( 1608) link_BETA1-4 : bond 0.00959 ( 8) link_BETA1-4 : angle 3.39396 ( 24) link_NAG-ASN : bond 0.01217 ( 28) link_NAG-ASN : angle 4.27086 ( 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: 27 poor density : 943 time to evaluate : 1.320 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: 0.9232 (ttt) cc_final: 0.8885 (ttm) REVERT: A 97 ASN cc_start: 0.9035 (t0) cc_final: 0.8725 (t0) REVERT: A 121 MET cc_start: 0.8489 (mmt) cc_final: 0.7999 (mpp) REVERT: A 290 PHE cc_start: 0.9480 (m-80) cc_final: 0.8970 (m-80) REVERT: A 428 ARG cc_start: 0.5754 (mpt180) cc_final: 0.5110 (mtp85) REVERT: A 491 LYS cc_start: 0.9509 (mmpt) cc_final: 0.9272 (mmmt) REVERT: A 496 TYR cc_start: 0.7558 (m-80) cc_final: 0.7212 (m-80) REVERT: A 564 LEU cc_start: 0.8754 (tp) cc_final: 0.8240 (tt) REVERT: A 567 LYS cc_start: 0.9431 (mmpt) cc_final: 0.9154 (mmmt) REVERT: A 628 THR cc_start: 0.7710 (t) cc_final: 0.7221 (m) REVERT: A 666 MET cc_start: 0.8951 (ttm) cc_final: 0.8628 (ttm) REVERT: A 669 PHE cc_start: 0.8197 (m-10) cc_final: 0.7952 (m-10) REVERT: A 670 LEU cc_start: 0.9558 (mp) cc_final: 0.9251 (pp) REVERT: A 688 MET cc_start: 0.8839 (ppp) cc_final: 0.8494 (ppp) REVERT: A 800 TYR cc_start: 0.9044 (p90) cc_final: 0.8664 (p90) REVERT: A 870 PHE cc_start: 0.8465 (m-80) cc_final: 0.8191 (m-80) REVERT: A 931 LEU cc_start: 0.9229 (tp) cc_final: 0.8900 (tp) REVERT: A 975 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8462 (tp-100) REVERT: A 985 TYR cc_start: 0.8620 (m-80) cc_final: 0.8285 (m-10) REVERT: A 988 ASP cc_start: 0.9123 (m-30) cc_final: 0.8560 (m-30) REVERT: A 1028 PHE cc_start: 0.8451 (m-80) cc_final: 0.8241 (m-80) REVERT: A 1047 LYS cc_start: 0.9404 (ttmt) cc_final: 0.9174 (ptmm) REVERT: A 1057 PHE cc_start: 0.8658 (t80) cc_final: 0.8254 (t80) REVERT: A 1076 ASP cc_start: 0.8529 (p0) cc_final: 0.7892 (m-30) REVERT: A 1125 LEU cc_start: 0.9489 (mt) cc_final: 0.9140 (pp) REVERT: A 1132 TRP cc_start: 0.8996 (t60) cc_final: 0.8431 (t60) REVERT: A 1133 LYS cc_start: 0.9417 (ttmt) cc_final: 0.9183 (tptt) REVERT: A 1150 LEU cc_start: 0.9369 (mm) cc_final: 0.9061 (mm) REVERT: A 1154 PHE cc_start: 0.8512 (m-80) cc_final: 0.7044 (m-80) REVERT: A 1314 MET cc_start: 0.9172 (mpp) cc_final: 0.8965 (ptp) REVERT: A 1323 TYR cc_start: 0.7964 (t80) cc_final: 0.7706 (t80) REVERT: B 32 MET cc_start: 0.9125 (ttt) cc_final: 0.8634 (ttt) REVERT: B 50 LEU cc_start: 0.9065 (tt) cc_final: 0.8562 (tt) REVERT: B 121 MET cc_start: 0.8028 (tpp) cc_final: 0.6949 (tpp) REVERT: B 216 GLU cc_start: 0.8790 (pp20) cc_final: 0.8434 (pp20) REVERT: B 246 MET cc_start: 0.7254 (mtm) cc_final: 0.6640 (mtp) REVERT: B 310 GLN cc_start: 0.8532 (mp10) cc_final: 0.7936 (mp10) REVERT: B 316 TYR cc_start: 0.6848 (m-80) cc_final: 0.6445 (t80) REVERT: B 354 LYS cc_start: 0.8655 (tttp) cc_final: 0.7674 (mttt) REVERT: B 356 ASP cc_start: 0.9120 (m-30) cc_final: 0.8478 (p0) REVERT: B 389 ASN cc_start: 0.8360 (m110) cc_final: 0.8050 (m-40) REVERT: B 418 SER cc_start: 0.8700 (t) cc_final: 0.8449 (p) REVERT: B 496 TYR cc_start: 0.7921 (m-80) cc_final: 0.7402 (m-80) REVERT: B 543 TYR cc_start: 0.8399 (p90) cc_final: 0.7582 (p90) REVERT: B 545 VAL cc_start: 0.9086 (t) cc_final: 0.8735 (m) REVERT: B 552 ILE cc_start: 0.8719 (pt) cc_final: 0.8373 (pt) REVERT: B 598 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8540 (ttt-90) REVERT: B 635 ASN cc_start: 0.9123 (p0) cc_final: 0.8394 (p0) REVERT: B 669 PHE cc_start: 0.8644 (m-80) cc_final: 0.8375 (m-80) REVERT: B 734 TYR cc_start: 0.7893 (t80) cc_final: 0.7441 (t80) REVERT: B 786 LEU cc_start: 0.9151 (tp) cc_final: 0.8937 (mp) REVERT: B 858 TRP cc_start: 0.7726 (m-90) cc_final: 0.7170 (m-90) REVERT: B 870 PHE cc_start: 0.9226 (t80) cc_final: 0.8521 (t80) REVERT: B 877 LEU cc_start: 0.8204 (tt) cc_final: 0.7983 (tt) REVERT: B 901 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8599 (mmtt) REVERT: B 935 LEU cc_start: 0.7348 (mt) cc_final: 0.6862 (mt) REVERT: B 985 TYR cc_start: 0.9213 (m-80) cc_final: 0.8657 (m-80) REVERT: B 1072 GLN cc_start: 0.9142 (mt0) cc_final: 0.8411 (tt0) REVERT: B 1224 THR cc_start: 0.8564 (p) cc_final: 0.7953 (t) REVERT: B 1227 ASP cc_start: 0.8666 (m-30) cc_final: 0.7777 (p0) REVERT: B 1331 ASN cc_start: 0.6884 (m110) cc_final: 0.3938 (m110) REVERT: C 32 MET cc_start: 0.9233 (ttt) cc_final: 0.8888 (ttm) REVERT: C 97 ASN cc_start: 0.9059 (t0) cc_final: 0.8742 (t0) REVERT: C 121 MET cc_start: 0.8520 (mmt) cc_final: 0.8020 (mpp) REVERT: C 132 GLN cc_start: 0.9397 (tt0) cc_final: 0.9176 (tm-30) REVERT: C 290 PHE cc_start: 0.9485 (m-80) cc_final: 0.8980 (m-80) REVERT: C 428 ARG cc_start: 0.5771 (mpt180) cc_final: 0.5134 (mtp180) REVERT: C 491 LYS cc_start: 0.9513 (mmpt) cc_final: 0.9278 (mmmt) REVERT: C 496 TYR cc_start: 0.7552 (m-80) cc_final: 0.7198 (m-80) REVERT: C 564 LEU cc_start: 0.8746 (tp) cc_final: 0.8235 (tt) REVERT: C 567 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9162 (mmmt) REVERT: C 628 THR cc_start: 0.7703 (t) cc_final: 0.7217 (m) REVERT: C 666 MET cc_start: 0.8962 (ttm) cc_final: 0.8635 (ttm) REVERT: C 669 PHE cc_start: 0.8193 (m-10) cc_final: 0.7953 (m-10) REVERT: C 670 LEU cc_start: 0.9551 (mp) cc_final: 0.9242 (pp) REVERT: C 688 MET cc_start: 0.8807 (ppp) cc_final: 0.8473 (ppp) REVERT: C 800 TYR cc_start: 0.9004 (p90) cc_final: 0.8636 (p90) REVERT: C 931 LEU cc_start: 0.9236 (tp) cc_final: 0.8900 (tp) REVERT: C 975 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8478 (tp-100) REVERT: C 985 TYR cc_start: 0.8678 (m-80) cc_final: 0.8267 (m-10) REVERT: C 988 ASP cc_start: 0.9332 (m-30) cc_final: 0.8882 (m-30) REVERT: C 1028 PHE cc_start: 0.8458 (m-80) cc_final: 0.8250 (m-80) REVERT: C 1047 LYS cc_start: 0.9397 (ttmt) cc_final: 0.9174 (ptmm) REVERT: C 1057 PHE cc_start: 0.8717 (t80) cc_final: 0.8314 (t80) REVERT: C 1076 ASP cc_start: 0.8532 (p0) cc_final: 0.7895 (m-30) REVERT: C 1125 LEU cc_start: 0.9489 (mt) cc_final: 0.9240 (pp) REVERT: C 1128 LEU cc_start: 0.9353 (mt) cc_final: 0.9053 (mt) REVERT: C 1132 TRP cc_start: 0.8993 (t60) cc_final: 0.8426 (t60) REVERT: C 1133 LYS cc_start: 0.9405 (ttmt) cc_final: 0.9169 (tptt) REVERT: C 1150 LEU cc_start: 0.9374 (mm) cc_final: 0.9059 (mm) REVERT: C 1154 PHE cc_start: 0.8541 (m-80) cc_final: 0.7121 (m-80) REVERT: C 1314 MET cc_start: 0.9161 (mpp) cc_final: 0.8960 (ptp) REVERT: C 1323 TYR cc_start: 0.7957 (t80) cc_final: 0.7697 (t80) REVERT: D 32 MET cc_start: 0.9136 (ttt) cc_final: 0.8648 (ttt) REVERT: D 50 LEU cc_start: 0.9059 (tt) cc_final: 0.8577 (tt) REVERT: D 121 MET cc_start: 0.8049 (tpp) cc_final: 0.6968 (tpp) REVERT: D 216 GLU cc_start: 0.8806 (pp20) cc_final: 0.8447 (pp20) REVERT: D 246 MET cc_start: 0.7263 (mtm) cc_final: 0.6656 (mtp) REVERT: D 310 GLN cc_start: 0.8508 (mp10) cc_final: 0.7916 (mp10) REVERT: D 316 TYR cc_start: 0.6861 (m-80) cc_final: 0.6450 (t80) REVERT: D 354 LYS cc_start: 0.8658 (tttp) cc_final: 0.7680 (mttt) REVERT: D 356 ASP cc_start: 0.9133 (m-30) cc_final: 0.8484 (p0) REVERT: D 389 ASN cc_start: 0.8354 (m110) cc_final: 0.8041 (m-40) REVERT: D 418 SER cc_start: 0.8715 (t) cc_final: 0.8472 (p) REVERT: D 496 TYR cc_start: 0.7930 (m-80) cc_final: 0.7405 (m-80) REVERT: D 543 TYR cc_start: 0.8423 (p90) cc_final: 0.7616 (p90) REVERT: D 545 VAL cc_start: 0.9087 (t) cc_final: 0.8732 (m) REVERT: D 552 ILE cc_start: 0.8721 (pt) cc_final: 0.8364 (pt) REVERT: D 570 LEU cc_start: 0.9056 (tt) cc_final: 0.8837 (pt) REVERT: D 571 SER cc_start: 0.9205 (t) cc_final: 0.8960 (p) REVERT: D 598 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8539 (ttt-90) REVERT: D 635 ASN cc_start: 0.9118 (p0) cc_final: 0.8481 (p0) REVERT: D 669 PHE cc_start: 0.8631 (m-80) cc_final: 0.8371 (m-80) REVERT: D 734 TYR cc_start: 0.7889 (t80) cc_final: 0.7444 (t80) REVERT: D 786 LEU cc_start: 0.9145 (tp) cc_final: 0.8934 (mp) REVERT: D 858 TRP cc_start: 0.7734 (m-90) cc_final: 0.7171 (m-90) REVERT: D 870 PHE cc_start: 0.9226 (t80) cc_final: 0.8479 (t80) REVERT: D 877 LEU cc_start: 0.8201 (tt) cc_final: 0.7980 (tt) REVERT: D 901 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8603 (mmtt) REVERT: D 935 LEU cc_start: 0.7299 (mt) cc_final: 0.6679 (mt) REVERT: D 985 TYR cc_start: 0.9226 (m-80) cc_final: 0.8694 (m-80) REVERT: D 1072 GLN cc_start: 0.9178 (mt0) cc_final: 0.8330 (tt0) REVERT: D 1224 THR cc_start: 0.8578 (p) cc_final: 0.7980 (t) REVERT: D 1227 ASP cc_start: 0.8670 (m-30) cc_final: 0.7784 (p0) REVERT: D 1328 LEU cc_start: 0.9511 (tp) cc_final: 0.9194 (tp) REVERT: D 1331 ASN cc_start: 0.6691 (m110) cc_final: 0.3834 (m110) outliers start: 27 outliers final: 4 residues processed: 955 average time/residue: 0.2446 time to fit residues: 383.6945 Evaluate side-chains 684 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 680 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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: 20.0000 chunk 354 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 312 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 289 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 425 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 517 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN B 156 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** B 327 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 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 321 HIS ** 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 976 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN D 156 HIS ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.089862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068770 restraints weight = 175045.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071360 restraints weight = 123464.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073442 restraints weight = 93726.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075100 restraints weight = 74502.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.076426 restraints weight = 61345.448| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 41259 Z= 0.277 Angle : 0.909 14.045 56144 Z= 0.459 Chirality : 0.052 0.355 6471 Planarity : 0.006 0.080 7166 Dihedral : 8.417 74.165 6200 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.11 % Favored : 88.81 % Rotamer: Outliers : 0.22 % Allowed : 6.45 % Favored : 93.33 % 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: -3.64 (0.10), residues: 5084 helix: -0.43 (0.16), residues: 859 sheet: -2.24 (0.11), residues: 1761 loop : -3.31 (0.11), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C1271 TYR 0.022 0.002 TYR C1055 PHE 0.048 0.003 PHE B1049 TRP 0.024 0.004 TRP D 436 HIS 0.010 0.002 HIS D 321 Details of bonding type rmsd covalent geometry : bond 0.00576 (41179) covalent geometry : angle 0.88932 (55948) SS BOND : bond 0.00676 ( 44) SS BOND : angle 2.41816 ( 88) hydrogen bonds : bond 0.05302 ( 536) hydrogen bonds : angle 5.33253 ( 1608) link_BETA1-4 : bond 0.00883 ( 8) link_BETA1-4 : angle 2.85734 ( 24) link_NAG-ASN : bond 0.01113 ( 28) link_NAG-ASN : angle 4.13229 ( 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 894 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 884 time to evaluate : 1.591 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: 0.9364 (ttt) cc_final: 0.9107 (ttt) REVERT: A 98 GLU cc_start: 0.8867 (pm20) cc_final: 0.8656 (pm20) REVERT: A 121 MET cc_start: 0.8693 (mmt) cc_final: 0.8431 (mpp) REVERT: A 151 MET cc_start: 0.3433 (ttm) cc_final: 0.3197 (tpp) REVERT: A 183 LEU cc_start: 0.8334 (tp) cc_final: 0.8044 (tp) REVERT: A 209 LYS cc_start: 0.9491 (mtmt) cc_final: 0.8800 (mmtm) REVERT: A 229 PHE cc_start: 0.8798 (p90) cc_final: 0.8560 (p90) REVERT: A 251 CYS cc_start: 0.8469 (m) cc_final: 0.7970 (t) REVERT: A 290 PHE cc_start: 0.9488 (m-80) cc_final: 0.9075 (m-80) REVERT: A 428 ARG cc_start: 0.5890 (mpt180) cc_final: 0.5333 (mtp85) REVERT: A 464 MET cc_start: 0.9537 (tpt) cc_final: 0.9215 (ttm) REVERT: A 496 TYR cc_start: 0.7795 (m-80) cc_final: 0.7502 (m-80) REVERT: A 564 LEU cc_start: 0.8594 (tp) cc_final: 0.7711 (tt) REVERT: A 567 LYS cc_start: 0.9541 (mmpt) cc_final: 0.9290 (mmmt) REVERT: A 627 LEU cc_start: 0.8441 (mm) cc_final: 0.7869 (mt) REVERT: A 666 MET cc_start: 0.9051 (ttm) cc_final: 0.8598 (ptm) REVERT: A 669 PHE cc_start: 0.8321 (m-10) cc_final: 0.7998 (m-10) REVERT: A 800 TYR cc_start: 0.9049 (p90) cc_final: 0.8726 (p90) REVERT: A 870 PHE cc_start: 0.8733 (m-80) cc_final: 0.8445 (m-80) REVERT: A 931 LEU cc_start: 0.9118 (tp) cc_final: 0.8839 (tp) REVERT: A 933 LEU cc_start: 0.9207 (mt) cc_final: 0.8937 (mt) REVERT: A 961 ASN cc_start: 0.6684 (t0) cc_final: 0.6433 (p0) REVERT: A 975 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8542 (tp-100) REVERT: A 988 ASP cc_start: 0.9204 (m-30) cc_final: 0.8642 (m-30) REVERT: A 1028 PHE cc_start: 0.8587 (m-80) cc_final: 0.8372 (m-80) REVERT: A 1057 PHE cc_start: 0.8820 (t80) cc_final: 0.8462 (t80) REVERT: A 1076 ASP cc_start: 0.8586 (p0) cc_final: 0.7952 (m-30) REVERT: A 1144 VAL cc_start: 0.8648 (p) cc_final: 0.8364 (m) REVERT: A 1150 LEU cc_start: 0.9456 (mm) cc_final: 0.9123 (mm) REVERT: A 1154 PHE cc_start: 0.8731 (m-80) cc_final: 0.7973 (m-80) REVERT: A 1165 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 1323 TYR cc_start: 0.8109 (t80) cc_final: 0.7843 (t80) REVERT: B 50 LEU cc_start: 0.9143 (tt) cc_final: 0.8819 (tt) REVERT: B 121 MET cc_start: 0.8326 (tpp) cc_final: 0.7446 (tpp) REVERT: B 151 MET cc_start: 0.6475 (mtt) cc_final: 0.5742 (ttp) REVERT: B 290 PHE cc_start: 0.9098 (m-80) cc_final: 0.8871 (m-80) REVERT: B 354 LYS cc_start: 0.8721 (tttp) cc_final: 0.7769 (mttt) REVERT: B 356 ASP cc_start: 0.9191 (m-30) cc_final: 0.8902 (t0) REVERT: B 360 ARG cc_start: 0.8722 (mpt180) cc_final: 0.8371 (mpt-90) REVERT: B 389 ASN cc_start: 0.8859 (m110) cc_final: 0.8656 (m-40) REVERT: B 392 ASN cc_start: 0.9557 (p0) cc_final: 0.9352 (p0) REVERT: B 394 TYR cc_start: 0.8067 (t80) cc_final: 0.7750 (t80) REVERT: B 415 MET cc_start: 0.6151 (pmm) cc_final: 0.5308 (pmm) REVERT: B 418 SER cc_start: 0.9017 (t) cc_final: 0.8728 (p) REVERT: B 479 HIS cc_start: 0.9286 (m90) cc_final: 0.9085 (m90) REVERT: B 496 TYR cc_start: 0.8011 (m-80) cc_final: 0.7608 (m-80) REVERT: B 543 TYR cc_start: 0.8618 (p90) cc_final: 0.8323 (p90) REVERT: B 552 ILE cc_start: 0.9185 (pt) cc_final: 0.8690 (pt) REVERT: B 554 ASP cc_start: 0.7490 (t0) cc_final: 0.7288 (t0) REVERT: B 572 PHE cc_start: 0.8385 (p90) cc_final: 0.7932 (p90) REVERT: B 673 MET cc_start: 0.9248 (tpt) cc_final: 0.8998 (tpp) REVERT: B 737 GLU cc_start: 0.8565 (pm20) cc_final: 0.8350 (pp20) REVERT: B 858 TRP cc_start: 0.7713 (m-90) cc_final: 0.7329 (m-90) REVERT: B 870 PHE cc_start: 0.9308 (t80) cc_final: 0.9009 (t80) REVERT: B 901 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8656 (mmtt) REVERT: B 935 LEU cc_start: 0.7693 (mt) cc_final: 0.7266 (mp) REVERT: B 985 TYR cc_start: 0.9158 (m-80) cc_final: 0.8774 (m-80) REVERT: B 1112 ILE cc_start: 0.8406 (mt) cc_final: 0.8195 (mp) REVERT: B 1205 GLU cc_start: 0.8384 (pt0) cc_final: 0.7973 (tt0) REVERT: B 1223 PRO cc_start: 0.6674 (Cg_exo) cc_final: 0.6334 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8713 (p) cc_final: 0.8170 (t) REVERT: B 1227 ASP cc_start: 0.8973 (m-30) cc_final: 0.8578 (p0) REVERT: B 1328 LEU cc_start: 0.9490 (tp) cc_final: 0.9076 (tp) REVERT: B 1331 ASN cc_start: 0.6776 (m110) cc_final: 0.4466 (m110) REVERT: C 32 MET cc_start: 0.9359 (ttt) cc_final: 0.9077 (ttt) REVERT: C 98 GLU cc_start: 0.8851 (pm20) cc_final: 0.8640 (pm20) REVERT: C 121 MET cc_start: 0.8706 (mmt) cc_final: 0.8432 (mpp) REVERT: C 151 MET cc_start: 0.3463 (ttm) cc_final: 0.3217 (tpp) REVERT: C 183 LEU cc_start: 0.8356 (tp) cc_final: 0.8077 (tp) REVERT: C 209 LYS cc_start: 0.9496 (mtmt) cc_final: 0.8794 (mmtm) REVERT: C 229 PHE cc_start: 0.8807 (p90) cc_final: 0.8571 (p90) REVERT: C 251 CYS cc_start: 0.8450 (m) cc_final: 0.7962 (t) REVERT: C 290 PHE cc_start: 0.9487 (m-80) cc_final: 0.9102 (m-80) REVERT: C 428 ARG cc_start: 0.5910 (mpt180) cc_final: 0.5312 (mtt180) REVERT: C 464 MET cc_start: 0.9532 (tpt) cc_final: 0.9209 (ttm) REVERT: C 496 TYR cc_start: 0.7800 (m-80) cc_final: 0.7497 (m-80) REVERT: C 564 LEU cc_start: 0.8590 (tp) cc_final: 0.7705 (tt) REVERT: C 567 LYS cc_start: 0.9549 (mmpt) cc_final: 0.9300 (mmmt) REVERT: C 627 LEU cc_start: 0.8420 (mm) cc_final: 0.7847 (mt) REVERT: C 666 MET cc_start: 0.9066 (ttm) cc_final: 0.8611 (ptm) REVERT: C 669 PHE cc_start: 0.8315 (m-10) cc_final: 0.7994 (m-10) REVERT: C 800 TYR cc_start: 0.9023 (p90) cc_final: 0.8758 (p90) REVERT: C 931 LEU cc_start: 0.9131 (tp) cc_final: 0.8852 (tp) REVERT: C 933 LEU cc_start: 0.9214 (mt) cc_final: 0.8946 (mt) REVERT: C 961 ASN cc_start: 0.6762 (t0) cc_final: 0.6552 (p0) REVERT: C 962 THR cc_start: 0.4967 (p) cc_final: 0.4742 (p) REVERT: C 975 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8556 (tp-100) REVERT: C 988 ASP cc_start: 0.9121 (m-30) cc_final: 0.8813 (m-30) REVERT: C 1028 PHE cc_start: 0.8597 (m-80) cc_final: 0.8391 (m-80) REVERT: C 1057 PHE cc_start: 0.8911 (t80) cc_final: 0.8492 (t80) REVERT: C 1076 ASP cc_start: 0.8596 (p0) cc_final: 0.7971 (m-30) REVERT: C 1150 LEU cc_start: 0.9463 (mm) cc_final: 0.9121 (mm) REVERT: C 1154 PHE cc_start: 0.8752 (m-80) cc_final: 0.8002 (m-80) REVERT: C 1165 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8045 (tm-30) REVERT: C 1271 ARG cc_start: 0.7501 (mtt90) cc_final: 0.7187 (mtt90) REVERT: C 1323 TYR cc_start: 0.8139 (t80) cc_final: 0.7888 (t80) REVERT: D 50 LEU cc_start: 0.9144 (tt) cc_final: 0.8861 (tt) REVERT: D 121 MET cc_start: 0.8315 (tpp) cc_final: 0.7426 (tpp) REVERT: D 151 MET cc_start: 0.6455 (mtt) cc_final: 0.5733 (ttp) REVERT: D 290 PHE cc_start: 0.9103 (m-80) cc_final: 0.8868 (m-80) REVERT: D 320 LEU cc_start: 0.8866 (mp) cc_final: 0.8655 (mp) REVERT: D 354 LYS cc_start: 0.8730 (tttp) cc_final: 0.7778 (mttt) REVERT: D 356 ASP cc_start: 0.9195 (m-30) cc_final: 0.8911 (t0) REVERT: D 360 ARG cc_start: 0.8708 (mpt180) cc_final: 0.8365 (mpt-90) REVERT: D 389 ASN cc_start: 0.8843 (m110) cc_final: 0.8632 (m-40) REVERT: D 392 ASN cc_start: 0.9533 (p0) cc_final: 0.9329 (p0) REVERT: D 394 TYR cc_start: 0.7960 (t80) cc_final: 0.7457 (t80) REVERT: D 415 MET cc_start: 0.6175 (pmm) cc_final: 0.5328 (pmm) REVERT: D 418 SER cc_start: 0.9038 (t) cc_final: 0.8739 (p) REVERT: D 479 HIS cc_start: 0.9292 (m90) cc_final: 0.9090 (m90) REVERT: D 496 TYR cc_start: 0.8009 (m-80) cc_final: 0.7606 (m-80) REVERT: D 543 TYR cc_start: 0.8624 (p90) cc_final: 0.8333 (p90) REVERT: D 552 ILE cc_start: 0.9180 (pt) cc_final: 0.8687 (pt) REVERT: D 571 SER cc_start: 0.9277 (t) cc_final: 0.9056 (p) REVERT: D 572 PHE cc_start: 0.8343 (p90) cc_final: 0.7990 (p90) REVERT: D 673 MET cc_start: 0.9225 (tpt) cc_final: 0.9002 (tpp) REVERT: D 737 GLU cc_start: 0.8555 (pm20) cc_final: 0.8340 (pp20) REVERT: D 858 TRP cc_start: 0.7759 (m-90) cc_final: 0.7372 (m-90) REVERT: D 870 PHE cc_start: 0.9341 (t80) cc_final: 0.8991 (t80) REVERT: D 901 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8682 (mmtt) REVERT: D 935 LEU cc_start: 0.7579 (mt) cc_final: 0.7200 (mp) REVERT: D 985 TYR cc_start: 0.9248 (m-80) cc_final: 0.8900 (m-80) REVERT: D 1112 ILE cc_start: 0.8385 (mt) cc_final: 0.8170 (mp) REVERT: D 1205 GLU cc_start: 0.8375 (pt0) cc_final: 0.7961 (tt0) REVERT: D 1223 PRO cc_start: 0.6621 (Cg_exo) cc_final: 0.6288 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8712 (p) cc_final: 0.8155 (t) REVERT: D 1227 ASP cc_start: 0.8970 (m-30) cc_final: 0.8572 (p0) REVERT: D 1328 LEU cc_start: 0.9531 (tp) cc_final: 0.9134 (tp) REVERT: D 1331 ASN cc_start: 0.6687 (m110) cc_final: 0.4427 (m110) REVERT: D 1333 LEU cc_start: 0.9085 (tp) cc_final: 0.8883 (tp) outliers start: 10 outliers final: 0 residues processed: 890 average time/residue: 0.2446 time to fit residues: 358.8796 Evaluate side-chains 660 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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: 6.9990 chunk 230 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 428 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 460 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 976 ASN B 263 HIS ** B 327 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 483 ASN ** 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** ** 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 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** D 327 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 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 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** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.090187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.068899 restraints weight = 173608.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.071486 restraints weight = 122537.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.073549 restraints weight = 93149.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075175 restraints weight = 74250.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076514 restraints weight = 61415.198| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 41259 Z= 0.192 Angle : 0.808 12.190 56144 Z= 0.405 Chirality : 0.050 0.400 6471 Planarity : 0.005 0.065 7166 Dihedral : 8.009 63.748 6200 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.37 % Favored : 89.56 % Rotamer: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % 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: -3.24 (0.11), residues: 5084 helix: -0.12 (0.17), residues: 869 sheet: -1.85 (0.12), residues: 1674 loop : -3.17 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1073 TYR 0.028 0.002 TYR D 316 PHE 0.043 0.002 PHE B1049 TRP 0.038 0.003 TRP B 436 HIS 0.008 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00408 (41179) covalent geometry : angle 0.79251 (55948) SS BOND : bond 0.00545 ( 44) SS BOND : angle 2.00370 ( 88) hydrogen bonds : bond 0.04965 ( 536) hydrogen bonds : angle 5.00483 ( 1608) link_BETA1-4 : bond 0.00928 ( 8) link_BETA1-4 : angle 2.37178 ( 24) link_NAG-ASN : bond 0.00778 ( 28) link_NAG-ASN : angle 3.55365 ( 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 875 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 869 time to evaluate : 1.515 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: 0.9354 (ttt) cc_final: 0.9078 (ttt) REVERT: A 121 MET cc_start: 0.8818 (mmt) cc_final: 0.8481 (mpp) REVERT: A 151 MET cc_start: 0.3882 (ttm) cc_final: 0.3422 (tpp) REVERT: A 290 PHE cc_start: 0.9467 (m-80) cc_final: 0.9121 (m-80) REVERT: A 309 PHE cc_start: 0.9103 (m-80) cc_final: 0.8750 (m-10) REVERT: A 373 ASP cc_start: 0.7948 (t0) cc_final: 0.7534 (t0) REVERT: A 428 ARG cc_start: 0.5818 (mpt180) cc_final: 0.5256 (mtt180) REVERT: A 464 MET cc_start: 0.9515 (tpt) cc_final: 0.9156 (ttm) REVERT: A 496 TYR cc_start: 0.7788 (m-80) cc_final: 0.7505 (m-80) REVERT: A 523 HIS cc_start: 0.9045 (m-70) cc_final: 0.8786 (m-70) REVERT: A 567 LYS cc_start: 0.9503 (mmpt) cc_final: 0.9240 (mmmt) REVERT: A 573 SER cc_start: 0.9281 (t) cc_final: 0.9010 (p) REVERT: A 627 LEU cc_start: 0.8721 (mm) cc_final: 0.8228 (mp) REVERT: A 666 MET cc_start: 0.9145 (ttm) cc_final: 0.8709 (ptm) REVERT: A 669 PHE cc_start: 0.8323 (m-10) cc_final: 0.8100 (m-10) REVERT: A 800 TYR cc_start: 0.9010 (p90) cc_final: 0.8711 (p90) REVERT: A 870 PHE cc_start: 0.8749 (m-80) cc_final: 0.8360 (m-80) REVERT: A 975 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8425 (tp-100) REVERT: A 988 ASP cc_start: 0.8885 (m-30) cc_final: 0.8401 (m-30) REVERT: A 1028 PHE cc_start: 0.8577 (m-80) cc_final: 0.8335 (m-80) REVERT: A 1057 PHE cc_start: 0.8792 (t80) cc_final: 0.8395 (t80) REVERT: A 1076 ASP cc_start: 0.8476 (p0) cc_final: 0.7837 (m-30) REVERT: A 1128 LEU cc_start: 0.9497 (mt) cc_final: 0.9269 (mt) REVERT: A 1132 TRP cc_start: 0.8704 (t60) cc_final: 0.7843 (t60) REVERT: A 1133 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9204 (tppt) REVERT: A 1150 LEU cc_start: 0.9429 (mm) cc_final: 0.9152 (pp) REVERT: A 1154 PHE cc_start: 0.9049 (m-80) cc_final: 0.7957 (m-80) REVERT: A 1165 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 121 MET cc_start: 0.8431 (tpp) cc_final: 0.7679 (tpp) REVERT: B 151 MET cc_start: 0.6372 (mtt) cc_final: 0.6137 (ttp) REVERT: B 216 GLU cc_start: 0.9040 (pp20) cc_final: 0.8718 (pp20) REVERT: B 290 PHE cc_start: 0.8952 (m-80) cc_final: 0.8730 (m-80) REVERT: B 354 LYS cc_start: 0.8541 (tttp) cc_final: 0.7657 (mttt) REVERT: B 356 ASP cc_start: 0.9168 (m-30) cc_final: 0.8827 (t0) REVERT: B 360 ARG cc_start: 0.8733 (mpt180) cc_final: 0.8378 (mpt-90) REVERT: B 389 ASN cc_start: 0.8793 (m110) cc_final: 0.8507 (m-40) REVERT: B 394 TYR cc_start: 0.8011 (t80) cc_final: 0.7709 (t80) REVERT: B 415 MET cc_start: 0.6498 (pmm) cc_final: 0.5191 (pmm) REVERT: B 418 SER cc_start: 0.9087 (t) cc_final: 0.8728 (p) REVERT: B 479 HIS cc_start: 0.9251 (m90) cc_final: 0.9022 (m90) REVERT: B 496 TYR cc_start: 0.7929 (m-80) cc_final: 0.7497 (m-80) REVERT: B 521 LYS cc_start: 0.8289 (mttt) cc_final: 0.8046 (mttt) REVERT: B 543 TYR cc_start: 0.8744 (p90) cc_final: 0.8160 (p90) REVERT: B 545 VAL cc_start: 0.8952 (t) cc_final: 0.8342 (t) REVERT: B 552 ILE cc_start: 0.9246 (pt) cc_final: 0.8841 (pt) REVERT: B 572 PHE cc_start: 0.8371 (p90) cc_final: 0.8003 (p90) REVERT: B 737 GLU cc_start: 0.8412 (pm20) cc_final: 0.8106 (pm20) REVERT: B 772 LEU cc_start: 0.9314 (mp) cc_final: 0.9103 (mp) REVERT: B 858 TRP cc_start: 0.7713 (m-90) cc_final: 0.7344 (m-90) REVERT: B 901 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8497 (mmtt) REVERT: B 965 LEU cc_start: 0.9170 (mt) cc_final: 0.8778 (mt) REVERT: B 985 TYR cc_start: 0.9041 (m-80) cc_final: 0.8739 (m-80) REVERT: B 1072 GLN cc_start: 0.9107 (mt0) cc_final: 0.8371 (tt0) REVERT: B 1112 ILE cc_start: 0.8370 (mt) cc_final: 0.8132 (mp) REVERT: B 1133 LYS cc_start: 0.9333 (mmpt) cc_final: 0.9125 (mmtm) REVERT: B 1205 GLU cc_start: 0.8296 (pt0) cc_final: 0.8017 (tt0) REVERT: B 1223 PRO cc_start: 0.6494 (Cg_exo) cc_final: 0.6096 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8688 (p) cc_final: 0.8192 (t) REVERT: B 1227 ASP cc_start: 0.9157 (m-30) cc_final: 0.8935 (p0) REVERT: B 1328 LEU cc_start: 0.9487 (tp) cc_final: 0.8877 (tp) REVERT: B 1330 TYR cc_start: 0.8950 (p90) cc_final: 0.8676 (p90) REVERT: B 1331 ASN cc_start: 0.6412 (m110) cc_final: 0.4094 (m110) REVERT: C 32 MET cc_start: 0.9337 (ttt) cc_final: 0.9056 (ttt) REVERT: C 121 MET cc_start: 0.8822 (mmt) cc_final: 0.8493 (mpp) REVERT: C 131 VAL cc_start: 0.9381 (t) cc_final: 0.8943 (t) REVERT: C 146 PHE cc_start: 0.9324 (p90) cc_final: 0.8984 (p90) REVERT: C 151 MET cc_start: 0.3900 (ttm) cc_final: 0.3433 (tpp) REVERT: C 183 LEU cc_start: 0.8375 (tp) cc_final: 0.8100 (tp) REVERT: C 290 PHE cc_start: 0.9457 (m-80) cc_final: 0.9082 (m-80) REVERT: C 309 PHE cc_start: 0.9057 (m-80) cc_final: 0.8814 (m-10) REVERT: C 312 LYS cc_start: 0.9468 (mmpt) cc_final: 0.9145 (mptt) REVERT: C 373 ASP cc_start: 0.7980 (t0) cc_final: 0.7524 (t0) REVERT: C 428 ARG cc_start: 0.5759 (mpt180) cc_final: 0.5243 (mtm180) REVERT: C 464 MET cc_start: 0.9513 (tpt) cc_final: 0.9151 (ttm) REVERT: C 496 TYR cc_start: 0.7778 (m-80) cc_final: 0.7495 (m-80) REVERT: C 523 HIS cc_start: 0.9057 (m-70) cc_final: 0.8794 (m-70) REVERT: C 567 LYS cc_start: 0.9493 (mmpt) cc_final: 0.9231 (mmmt) REVERT: C 573 SER cc_start: 0.9284 (t) cc_final: 0.9012 (p) REVERT: C 627 LEU cc_start: 0.8707 (mm) cc_final: 0.8216 (mp) REVERT: C 666 MET cc_start: 0.9160 (ttm) cc_final: 0.8723 (ptm) REVERT: C 669 PHE cc_start: 0.8323 (m-10) cc_final: 0.8097 (m-10) REVERT: C 798 MET cc_start: 0.8552 (ppp) cc_final: 0.8090 (ppp) REVERT: C 800 TYR cc_start: 0.8977 (p90) cc_final: 0.8717 (p90) REVERT: C 975 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8438 (tp-100) REVERT: C 988 ASP cc_start: 0.9208 (m-30) cc_final: 0.8853 (m-30) REVERT: C 1028 PHE cc_start: 0.8582 (m-80) cc_final: 0.8343 (m-80) REVERT: C 1057 PHE cc_start: 0.8744 (t80) cc_final: 0.8354 (t80) REVERT: C 1076 ASP cc_start: 0.8481 (p0) cc_final: 0.7856 (m-30) REVERT: C 1125 LEU cc_start: 0.9680 (mt) cc_final: 0.9470 (pp) REVERT: C 1132 TRP cc_start: 0.8713 (t60) cc_final: 0.7890 (t60) REVERT: C 1133 LYS cc_start: 0.9447 (ttmt) cc_final: 0.9208 (tppt) REVERT: C 1150 LEU cc_start: 0.9443 (mm) cc_final: 0.9120 (mm) REVERT: C 1154 PHE cc_start: 0.9049 (m-80) cc_final: 0.7913 (m-80) REVERT: C 1165 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8223 (tm-30) REVERT: D 50 LEU cc_start: 0.9063 (tt) cc_final: 0.8834 (tt) REVERT: D 121 MET cc_start: 0.8419 (tpp) cc_final: 0.7660 (tpp) REVERT: D 151 MET cc_start: 0.6382 (mtt) cc_final: 0.6114 (ttp) REVERT: D 216 GLU cc_start: 0.9029 (pp20) cc_final: 0.8715 (pp20) REVERT: D 290 PHE cc_start: 0.8954 (m-80) cc_final: 0.8738 (m-80) REVERT: D 354 LYS cc_start: 0.8546 (tttp) cc_final: 0.7664 (mttt) REVERT: D 356 ASP cc_start: 0.9182 (m-30) cc_final: 0.8830 (t0) REVERT: D 360 ARG cc_start: 0.8746 (mpt180) cc_final: 0.8430 (mpt-90) REVERT: D 389 ASN cc_start: 0.8779 (m110) cc_final: 0.8476 (m-40) REVERT: D 394 TYR cc_start: 0.7835 (t80) cc_final: 0.7477 (t80) REVERT: D 415 MET cc_start: 0.6489 (pmm) cc_final: 0.5187 (pmm) REVERT: D 418 SER cc_start: 0.9095 (t) cc_final: 0.8716 (p) REVERT: D 461 LEU cc_start: 0.9279 (mp) cc_final: 0.9002 (mp) REVERT: D 479 HIS cc_start: 0.9255 (m90) cc_final: 0.9022 (m90) REVERT: D 496 TYR cc_start: 0.7921 (m-80) cc_final: 0.7478 (m-80) REVERT: D 521 LYS cc_start: 0.8275 (mttt) cc_final: 0.8034 (mttt) REVERT: D 543 TYR cc_start: 0.8759 (p90) cc_final: 0.8160 (p90) REVERT: D 545 VAL cc_start: 0.8957 (t) cc_final: 0.8346 (t) REVERT: D 552 ILE cc_start: 0.9246 (pt) cc_final: 0.8835 (pt) REVERT: D 554 ASP cc_start: 0.7458 (t0) cc_final: 0.7021 (t0) REVERT: D 571 SER cc_start: 0.9177 (t) cc_final: 0.8976 (p) REVERT: D 572 PHE cc_start: 0.8379 (p90) cc_final: 0.8034 (p90) REVERT: D 737 GLU cc_start: 0.8412 (pm20) cc_final: 0.8109 (pm20) REVERT: D 772 LEU cc_start: 0.9318 (mp) cc_final: 0.9113 (mp) REVERT: D 858 TRP cc_start: 0.7659 (m-90) cc_final: 0.7318 (m-90) REVERT: D 965 LEU cc_start: 0.9190 (mt) cc_final: 0.8784 (mt) REVERT: D 985 TYR cc_start: 0.9075 (m-80) cc_final: 0.8755 (m-80) REVERT: D 1072 GLN cc_start: 0.9197 (mt0) cc_final: 0.8532 (tt0) REVERT: D 1112 ILE cc_start: 0.8357 (mt) cc_final: 0.8116 (mp) REVERT: D 1133 LYS cc_start: 0.9331 (mmpt) cc_final: 0.9118 (mmtt) REVERT: D 1205 GLU cc_start: 0.8303 (pt0) cc_final: 0.8034 (tt0) REVERT: D 1223 PRO cc_start: 0.6440 (Cg_exo) cc_final: 0.6018 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8669 (p) cc_final: 0.8168 (t) REVERT: D 1227 ASP cc_start: 0.9158 (m-30) cc_final: 0.8928 (p0) REVERT: D 1330 TYR cc_start: 0.8975 (p90) cc_final: 0.8752 (p90) REVERT: D 1331 ASN cc_start: 0.6457 (m110) cc_final: 0.4394 (m110) outliers start: 6 outliers final: 0 residues processed: 873 average time/residue: 0.2324 time to fit residues: 334.9899 Evaluate side-chains 700 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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: 30.0000 chunk 430 optimal weight: 0.8980 chunk 333 optimal weight: 0.0470 chunk 258 optimal weight: 0.0770 chunk 447 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 210 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 1.9638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** 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** 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 321 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** D1017 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.090816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069230 restraints weight = 168989.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071871 restraints weight = 119339.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.073972 restraints weight = 90786.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.075649 restraints weight = 72363.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.076974 restraints weight = 59665.719| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41259 Z= 0.158 Angle : 0.779 12.021 56144 Z= 0.386 Chirality : 0.050 0.360 6471 Planarity : 0.005 0.059 7166 Dihedral : 7.734 59.635 6200 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.39 % Favored : 89.54 % Rotamer: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % 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: -3.00 (0.11), residues: 5084 helix: 0.11 (0.17), residues: 871 sheet: -1.64 (0.12), residues: 1672 loop : -3.07 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1271 TYR 0.047 0.002 TYR B1152 PHE 0.047 0.002 PHE B 669 TRP 0.053 0.003 TRP B 739 HIS 0.006 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00348 (41179) covalent geometry : angle 0.76114 (55948) SS BOND : bond 0.00813 ( 44) SS BOND : angle 2.02852 ( 88) hydrogen bonds : bond 0.04850 ( 536) hydrogen bonds : angle 4.86801 ( 1608) link_BETA1-4 : bond 0.01097 ( 8) link_BETA1-4 : angle 2.45419 ( 24) link_NAG-ASN : bond 0.00861 ( 28) link_NAG-ASN : angle 3.63238 ( 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 878 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 876 time to evaluate : 1.481 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: A 32 MET cc_start: 0.9357 (ttt) cc_final: 0.9072 (ttt) REVERT: A 50 LEU cc_start: 0.9153 (tt) cc_final: 0.8389 (mm) REVERT: A 121 MET cc_start: 0.8884 (mmt) cc_final: 0.8503 (mpp) REVERT: A 183 LEU cc_start: 0.8432 (tp) cc_final: 0.8160 (tp) REVERT: A 209 LYS cc_start: 0.9448 (mtmt) cc_final: 0.8667 (mmtm) REVERT: A 251 CYS cc_start: 0.8315 (m) cc_final: 0.8006 (t) REVERT: A 289 LYS cc_start: 0.9438 (mppt) cc_final: 0.9234 (mmmt) REVERT: A 290 PHE cc_start: 0.9446 (m-80) cc_final: 0.9090 (m-80) REVERT: A 312 LYS cc_start: 0.9456 (mmpt) cc_final: 0.9101 (mppt) REVERT: A 373 ASP cc_start: 0.7974 (t0) cc_final: 0.7595 (t0) REVERT: A 428 ARG cc_start: 0.5685 (mpt180) cc_final: 0.5142 (mtp180) REVERT: A 464 MET cc_start: 0.9470 (tpt) cc_final: 0.9132 (ttm) REVERT: A 491 LYS cc_start: 0.9413 (mmpt) cc_final: 0.9176 (mmmt) REVERT: A 523 HIS cc_start: 0.9096 (m-70) cc_final: 0.8865 (m-70) REVERT: A 567 LYS cc_start: 0.9537 (mmpt) cc_final: 0.9287 (mmmt) REVERT: A 582 HIS cc_start: 0.9170 (t70) cc_final: 0.8666 (p-80) REVERT: A 627 LEU cc_start: 0.8787 (mm) cc_final: 0.8252 (mp) REVERT: A 666 MET cc_start: 0.9136 (ttm) cc_final: 0.8637 (ptp) REVERT: A 669 PHE cc_start: 0.8350 (m-10) cc_final: 0.8138 (m-10) REVERT: A 800 TYR cc_start: 0.8969 (p90) cc_final: 0.8695 (p90) REVERT: A 870 PHE cc_start: 0.8721 (m-80) cc_final: 0.8289 (m-80) REVERT: A 962 THR cc_start: 0.5073 (p) cc_final: 0.4849 (p) REVERT: A 975 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8477 (tp-100) REVERT: A 988 ASP cc_start: 0.8881 (m-30) cc_final: 0.8448 (m-30) REVERT: A 1028 PHE cc_start: 0.8449 (m-80) cc_final: 0.8099 (t80) REVERT: A 1057 PHE cc_start: 0.8783 (t80) cc_final: 0.8392 (t80) REVERT: A 1076 ASP cc_start: 0.8425 (p0) cc_final: 0.7815 (m-30) REVERT: A 1132 TRP cc_start: 0.8704 (t60) cc_final: 0.7842 (t60) REVERT: A 1133 LYS cc_start: 0.9447 (ttmt) cc_final: 0.9200 (tppt) REVERT: A 1144 VAL cc_start: 0.8295 (p) cc_final: 0.7938 (m) REVERT: A 1150 LEU cc_start: 0.9453 (mm) cc_final: 0.9172 (pp) REVERT: A 1154 PHE cc_start: 0.9052 (m-80) cc_final: 0.8024 (m-80) REVERT: A 1165 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 1323 TYR cc_start: 0.8285 (t80) cc_final: 0.7900 (t80) REVERT: B 32 MET cc_start: 0.9163 (tpt) cc_final: 0.8886 (tpt) REVERT: B 50 LEU cc_start: 0.9004 (tt) cc_final: 0.8744 (tt) REVERT: B 121 MET cc_start: 0.8524 (tpp) cc_final: 0.7797 (tpp) REVERT: B 134 ASP cc_start: 0.8885 (t70) cc_final: 0.8499 (t70) REVERT: B 216 GLU cc_start: 0.9030 (pp20) cc_final: 0.8721 (pp20) REVERT: B 290 PHE cc_start: 0.8987 (m-80) cc_final: 0.8766 (m-80) REVERT: B 301 TYR cc_start: 0.8635 (m-80) cc_final: 0.8409 (m-10) REVERT: B 354 LYS cc_start: 0.8484 (tttp) cc_final: 0.7623 (mttt) REVERT: B 356 ASP cc_start: 0.9193 (m-30) cc_final: 0.8842 (t0) REVERT: B 360 ARG cc_start: 0.8592 (mpt180) cc_final: 0.8257 (mpt-90) REVERT: B 389 ASN cc_start: 0.8754 (m110) cc_final: 0.8367 (m-40) REVERT: B 394 TYR cc_start: 0.7949 (t80) cc_final: 0.7655 (t80) REVERT: B 415 MET cc_start: 0.6618 (pmm) cc_final: 0.5069 (pmm) REVERT: B 418 SER cc_start: 0.9019 (t) cc_final: 0.8515 (p) REVERT: B 461 LEU cc_start: 0.9276 (mp) cc_final: 0.8967 (mm) REVERT: B 479 HIS cc_start: 0.9212 (m90) cc_final: 0.8983 (m90) REVERT: B 496 TYR cc_start: 0.7895 (m-80) cc_final: 0.7501 (m-80) REVERT: B 521 LYS cc_start: 0.8260 (mttt) cc_final: 0.7992 (mttt) REVERT: B 539 ARG cc_start: 0.7752 (ttm170) cc_final: 0.6656 (ttt180) REVERT: B 543 TYR cc_start: 0.8735 (p90) cc_final: 0.8125 (p90) REVERT: B 545 VAL cc_start: 0.8880 (t) cc_final: 0.8202 (t) REVERT: B 552 ILE cc_start: 0.9275 (pt) cc_final: 0.8859 (pt) REVERT: B 554 ASP cc_start: 0.7384 (t0) cc_final: 0.6729 (t0) REVERT: B 572 PHE cc_start: 0.8340 (p90) cc_final: 0.8070 (p90) REVERT: B 628 THR cc_start: 0.8896 (p) cc_final: 0.8559 (p) REVERT: B 635 ASN cc_start: 0.9281 (p0) cc_final: 0.8814 (p0) REVERT: B 770 PHE cc_start: 0.8972 (t80) cc_final: 0.8718 (t80) REVERT: B 796 LEU cc_start: 0.8751 (pp) cc_final: 0.8201 (pp) REVERT: B 798 MET cc_start: 0.8231 (mpp) cc_final: 0.7905 (mpp) REVERT: B 870 PHE cc_start: 0.9248 (t80) cc_final: 0.8995 (t80) REVERT: B 901 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8425 (mmtt) REVERT: B 965 LEU cc_start: 0.9193 (mt) cc_final: 0.8793 (mt) REVERT: B 985 TYR cc_start: 0.9128 (m-80) cc_final: 0.8769 (m-80) REVERT: B 1072 GLN cc_start: 0.9152 (mt0) cc_final: 0.8357 (tt0) REVERT: B 1165 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8777 (tt0) REVERT: B 1205 GLU cc_start: 0.8343 (pt0) cc_final: 0.8022 (tt0) REVERT: B 1223 PRO cc_start: 0.6570 (Cg_exo) cc_final: 0.6217 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8643 (p) cc_final: 0.8184 (t) REVERT: B 1241 GLN cc_start: 0.7503 (mp-120) cc_final: 0.7133 (mm-40) REVERT: B 1328 LEU cc_start: 0.9464 (tp) cc_final: 0.9056 (tp) REVERT: B 1330 TYR cc_start: 0.8997 (p90) cc_final: 0.8759 (p90) REVERT: B 1331 ASN cc_start: 0.6380 (m110) cc_final: 0.4090 (m110) REVERT: C 32 MET cc_start: 0.9357 (ttt) cc_final: 0.9097 (ttt) REVERT: C 50 LEU cc_start: 0.9140 (tt) cc_final: 0.8386 (mm) REVERT: C 121 MET cc_start: 0.8926 (mmt) cc_final: 0.8522 (mpp) REVERT: C 131 VAL cc_start: 0.9312 (t) cc_final: 0.8858 (t) REVERT: C 146 PHE cc_start: 0.9314 (p90) cc_final: 0.8968 (p90) REVERT: C 183 LEU cc_start: 0.8492 (tp) cc_final: 0.8224 (tp) REVERT: C 209 LYS cc_start: 0.9451 (mtmt) cc_final: 0.8671 (mmtm) REVERT: C 289 LYS cc_start: 0.9448 (mppt) cc_final: 0.9245 (mmmt) REVERT: C 290 PHE cc_start: 0.9455 (m-80) cc_final: 0.9064 (m-80) REVERT: C 312 LYS cc_start: 0.9447 (mmpt) cc_final: 0.9169 (mptt) REVERT: C 373 ASP cc_start: 0.7984 (t0) cc_final: 0.7554 (t0) REVERT: C 428 ARG cc_start: 0.5659 (mpt180) cc_final: 0.5128 (mtt180) REVERT: C 464 MET cc_start: 0.9457 (tpt) cc_final: 0.9040 (ttm) REVERT: C 491 LYS cc_start: 0.9418 (mmpt) cc_final: 0.9184 (mmmt) REVERT: C 523 HIS cc_start: 0.9107 (m-70) cc_final: 0.8875 (m-70) REVERT: C 567 LYS cc_start: 0.9546 (mmpt) cc_final: 0.9297 (mmmt) REVERT: C 582 HIS cc_start: 0.9165 (t70) cc_final: 0.8657 (p-80) REVERT: C 626 ASP cc_start: 0.8634 (p0) cc_final: 0.7820 (t0) REVERT: C 627 LEU cc_start: 0.8759 (mm) cc_final: 0.8193 (mp) REVERT: C 666 MET cc_start: 0.9143 (ttm) cc_final: 0.8648 (ptp) REVERT: C 669 PHE cc_start: 0.8348 (m-10) cc_final: 0.8134 (m-10) REVERT: C 798 MET cc_start: 0.8560 (ppp) cc_final: 0.8185 (ppp) REVERT: C 800 TYR cc_start: 0.8920 (p90) cc_final: 0.8702 (p90) REVERT: C 962 THR cc_start: 0.5049 (p) cc_final: 0.4786 (p) REVERT: C 975 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8461 (tp-100) REVERT: C 1028 PHE cc_start: 0.8471 (m-80) cc_final: 0.8157 (t80) REVERT: C 1057 PHE cc_start: 0.8727 (t80) cc_final: 0.8320 (t80) REVERT: C 1076 ASP cc_start: 0.8431 (p0) cc_final: 0.7836 (m-30) REVERT: C 1132 TRP cc_start: 0.8709 (t60) cc_final: 0.7856 (t60) REVERT: C 1133 LYS cc_start: 0.9421 (ttmt) cc_final: 0.9177 (tppt) REVERT: C 1144 VAL cc_start: 0.8365 (p) cc_final: 0.8012 (m) REVERT: C 1150 LEU cc_start: 0.9467 (mm) cc_final: 0.9187 (pp) REVERT: C 1154 PHE cc_start: 0.9058 (m-80) cc_final: 0.7951 (m-80) REVERT: C 1165 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 1323 TYR cc_start: 0.8278 (t80) cc_final: 0.7890 (t80) REVERT: D 32 MET cc_start: 0.9192 (tpt) cc_final: 0.8941 (tpt) REVERT: D 121 MET cc_start: 0.8513 (tpp) cc_final: 0.7774 (tpp) REVERT: D 134 ASP cc_start: 0.8903 (t70) cc_final: 0.8502 (t70) REVERT: D 216 GLU cc_start: 0.9020 (pp20) cc_final: 0.8714 (pp20) REVERT: D 290 PHE cc_start: 0.8977 (m-80) cc_final: 0.8760 (m-80) REVERT: D 301 TYR cc_start: 0.8634 (m-80) cc_final: 0.8408 (m-10) REVERT: D 354 LYS cc_start: 0.8495 (tttp) cc_final: 0.7633 (mttt) REVERT: D 356 ASP cc_start: 0.9208 (m-30) cc_final: 0.8851 (t0) REVERT: D 360 ARG cc_start: 0.8602 (mpt180) cc_final: 0.8259 (mpt-90) REVERT: D 389 ASN cc_start: 0.8707 (m110) cc_final: 0.8459 (m-40) REVERT: D 394 TYR cc_start: 0.7816 (t80) cc_final: 0.7493 (t80) REVERT: D 415 MET cc_start: 0.6619 (pmm) cc_final: 0.5079 (pmm) REVERT: D 418 SER cc_start: 0.9024 (t) cc_final: 0.8719 (t) REVERT: D 461 LEU cc_start: 0.9294 (mp) cc_final: 0.8973 (mm) REVERT: D 479 HIS cc_start: 0.9207 (m90) cc_final: 0.8978 (m90) REVERT: D 496 TYR cc_start: 0.7861 (m-80) cc_final: 0.7410 (m-80) REVERT: D 521 LYS cc_start: 0.8246 (mttt) cc_final: 0.7977 (mttt) REVERT: D 539 ARG cc_start: 0.7740 (ttm170) cc_final: 0.6665 (ttt180) REVERT: D 543 TYR cc_start: 0.8751 (p90) cc_final: 0.8124 (p90) REVERT: D 545 VAL cc_start: 0.8869 (t) cc_final: 0.8251 (t) REVERT: D 552 ILE cc_start: 0.9266 (pt) cc_final: 0.8831 (pt) REVERT: D 554 ASP cc_start: 0.7470 (t0) cc_final: 0.6893 (t0) REVERT: D 571 SER cc_start: 0.9136 (t) cc_final: 0.8886 (p) REVERT: D 572 PHE cc_start: 0.8387 (p90) cc_final: 0.8044 (p90) REVERT: D 628 THR cc_start: 0.8909 (p) cc_final: 0.8576 (p) REVERT: D 635 ASN cc_start: 0.9272 (p0) cc_final: 0.8796 (p0) REVERT: D 770 PHE cc_start: 0.8958 (t80) cc_final: 0.8717 (t80) REVERT: D 796 LEU cc_start: 0.8763 (pp) cc_final: 0.8278 (pp) REVERT: D 798 MET cc_start: 0.8169 (mpp) cc_final: 0.7776 (mpp) REVERT: D 870 PHE cc_start: 0.9282 (t80) cc_final: 0.9040 (t80) REVERT: D 965 LEU cc_start: 0.9202 (mt) cc_final: 0.8816 (mt) REVERT: D 985 TYR cc_start: 0.9095 (m-80) cc_final: 0.8717 (m-80) REVERT: D 1072 GLN cc_start: 0.9181 (mt0) cc_final: 0.8457 (tt0) REVERT: D 1165 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8774 (tt0) REVERT: D 1205 GLU cc_start: 0.8341 (pt0) cc_final: 0.8023 (tt0) REVERT: D 1223 PRO cc_start: 0.6549 (Cg_exo) cc_final: 0.6186 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8640 (p) cc_final: 0.8170 (t) REVERT: D 1241 GLN cc_start: 0.7515 (mp-120) cc_final: 0.7145 (mm-40) REVERT: D 1328 LEU cc_start: 0.9509 (tp) cc_final: 0.8895 (tp) REVERT: D 1330 TYR cc_start: 0.9006 (p90) cc_final: 0.8668 (p90) REVERT: D 1331 ASN cc_start: 0.6378 (m110) cc_final: 0.4204 (m110) outliers start: 2 outliers final: 0 residues processed: 876 average time/residue: 0.2389 time to fit residues: 346.9240 Evaluate side-chains 698 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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: 5.9990 chunk 182 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 395 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 48 optimal weight: 40.0000 chunk 340 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN A1074 GLN A1242 GLN ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** B 477 GLN ** 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 827 GLN ** 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** C 132 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN C 994 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 GLN C1074 GLN C1242 GLN D 441 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN D1017 ASN D1089 ASN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 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 = 0.3651 r_free = 0.3651 target = 0.083359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063510 restraints weight = 185160.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065844 restraints weight = 130920.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067701 restraints weight = 99746.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069170 restraints weight = 79462.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070360 restraints weight = 65755.554| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 41259 Z= 0.270 Angle : 0.898 12.258 56144 Z= 0.458 Chirality : 0.052 0.353 6471 Planarity : 0.007 0.083 7166 Dihedral : 8.116 59.363 6200 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.25 % Favored : 87.67 % Rotamer: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.48 % 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: -3.38 (0.11), residues: 5084 helix: -0.33 (0.17), residues: 878 sheet: -2.04 (0.12), residues: 1759 loop : -3.16 (0.11), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 804 TYR 0.034 0.003 TYR B1152 PHE 0.051 0.003 PHE C1049 TRP 0.035 0.004 TRP A 739 HIS 0.013 0.002 HIS D 321 Details of bonding type rmsd covalent geometry : bond 0.00559 (41179) covalent geometry : angle 0.88197 (55948) SS BOND : bond 0.00620 ( 44) SS BOND : angle 1.89821 ( 88) hydrogen bonds : bond 0.05085 ( 536) hydrogen bonds : angle 5.29918 ( 1608) link_BETA1-4 : bond 0.00897 ( 8) link_BETA1-4 : angle 2.68583 ( 24) link_NAG-ASN : bond 0.00848 ( 28) link_NAG-ASN : angle 3.81259 ( 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 835 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 829 time to evaluate : 1.696 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: A 50 LEU cc_start: 0.9502 (tt) cc_final: 0.8864 (mm) REVERT: A 121 MET cc_start: 0.9022 (mmt) cc_final: 0.8646 (mpp) REVERT: A 137 ILE cc_start: 0.8910 (tt) cc_final: 0.8606 (tt) REVERT: A 151 MET cc_start: 0.4538 (ttm) cc_final: 0.4298 (ttm) REVERT: A 209 LYS cc_start: 0.9393 (mtmt) cc_final: 0.8559 (mmtm) REVERT: A 290 PHE cc_start: 0.9450 (m-80) cc_final: 0.9054 (m-80) REVERT: A 309 PHE cc_start: 0.9267 (m-80) cc_final: 0.8916 (m-80) REVERT: A 312 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9084 (mppt) REVERT: A 318 MET cc_start: 0.8198 (tpp) cc_final: 0.7721 (tpp) REVERT: A 373 ASP cc_start: 0.8336 (t0) cc_final: 0.8075 (t0) REVERT: A 428 ARG cc_start: 0.5998 (mpt180) cc_final: 0.5396 (mtt180) REVERT: A 462 GLU cc_start: 0.7819 (pt0) cc_final: 0.7523 (pm20) REVERT: A 464 MET cc_start: 0.9573 (tpt) cc_final: 0.9186 (ttm) REVERT: A 523 HIS cc_start: 0.9129 (m-70) cc_final: 0.8770 (m-70) REVERT: A 564 LEU cc_start: 0.8894 (tp) cc_final: 0.8259 (tt) REVERT: A 582 HIS cc_start: 0.9220 (t70) cc_final: 0.8902 (p-80) REVERT: A 627 LEU cc_start: 0.8828 (mm) cc_final: 0.8411 (mp) REVERT: A 666 MET cc_start: 0.9180 (ttm) cc_final: 0.8743 (ptp) REVERT: A 669 PHE cc_start: 0.8607 (m-10) cc_final: 0.8400 (m-80) REVERT: A 764 GLU cc_start: 0.6345 (mp0) cc_final: 0.5937 (mp0) REVERT: A 800 TYR cc_start: 0.9077 (p90) cc_final: 0.8736 (p90) REVERT: A 870 PHE cc_start: 0.8967 (m-80) cc_final: 0.8460 (m-80) REVERT: A 931 LEU cc_start: 0.8968 (tp) cc_final: 0.8590 (tt) REVERT: A 975 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8548 (tp-100) REVERT: A 988 ASP cc_start: 0.9128 (m-30) cc_final: 0.8678 (m-30) REVERT: A 1020 HIS cc_start: 0.9080 (t-90) cc_final: 0.8751 (t-90) REVERT: A 1028 PHE cc_start: 0.8559 (m-80) cc_final: 0.8319 (m-80) REVERT: A 1074 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8893 (tp-100) REVERT: A 1076 ASP cc_start: 0.8575 (p0) cc_final: 0.8128 (m-30) REVERT: A 1132 TRP cc_start: 0.8742 (t60) cc_final: 0.7873 (t60) REVERT: A 1133 LYS cc_start: 0.9478 (ttmt) cc_final: 0.9219 (tppt) REVERT: A 1150 LEU cc_start: 0.9516 (mm) cc_final: 0.9194 (pp) REVERT: A 1154 PHE cc_start: 0.9221 (m-80) cc_final: 0.8225 (m-80) REVERT: A 1165 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 1214 LEU cc_start: 0.9427 (mt) cc_final: 0.9198 (mt) REVERT: A 1323 TYR cc_start: 0.8488 (t80) cc_final: 0.7964 (t80) REVERT: B 121 MET cc_start: 0.8584 (tpp) cc_final: 0.8168 (tpt) REVERT: B 134 ASP cc_start: 0.8981 (t70) cc_final: 0.8616 (t70) REVERT: B 179 GLN cc_start: 0.8186 (pp30) cc_final: 0.7956 (pp30) REVERT: B 290 PHE cc_start: 0.9163 (m-80) cc_final: 0.8832 (m-80) REVERT: B 291 SER cc_start: 0.8836 (p) cc_final: 0.8414 (t) REVERT: B 360 ARG cc_start: 0.8796 (mpt180) cc_final: 0.8247 (mtt180) REVERT: B 389 ASN cc_start: 0.9068 (m110) cc_final: 0.8867 (m-40) REVERT: B 394 TYR cc_start: 0.8087 (t80) cc_final: 0.7719 (t80) REVERT: B 415 MET cc_start: 0.6946 (pmm) cc_final: 0.5431 (pmm) REVERT: B 461 LEU cc_start: 0.9197 (mp) cc_final: 0.8858 (mm) REVERT: B 496 TYR cc_start: 0.7982 (m-80) cc_final: 0.7710 (m-80) REVERT: B 521 LYS cc_start: 0.8231 (mttt) cc_final: 0.7982 (mttt) REVERT: B 543 TYR cc_start: 0.8675 (p90) cc_final: 0.8149 (p90) REVERT: B 552 ILE cc_start: 0.9409 (pt) cc_final: 0.9046 (pt) REVERT: B 586 ARG cc_start: 0.9044 (ttt90) cc_final: 0.8352 (tpp80) REVERT: B 798 MET cc_start: 0.8225 (mpp) cc_final: 0.7979 (mpp) REVERT: B 870 PHE cc_start: 0.9348 (t80) cc_final: 0.9104 (t80) REVERT: B 965 LEU cc_start: 0.9379 (mt) cc_final: 0.9095 (mt) REVERT: B 985 TYR cc_start: 0.9204 (m-80) cc_final: 0.8923 (m-80) REVERT: B 1072 GLN cc_start: 0.9167 (mt0) cc_final: 0.8508 (tt0) REVERT: B 1156 LEU cc_start: 0.8001 (mm) cc_final: 0.7659 (mm) REVERT: B 1165 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8992 (tt0) REVERT: B 1205 GLU cc_start: 0.8433 (pt0) cc_final: 0.8005 (tt0) REVERT: B 1241 GLN cc_start: 0.7724 (mp-120) cc_final: 0.7327 (mp10) REVERT: B 1330 TYR cc_start: 0.9131 (p90) cc_final: 0.8778 (p90) REVERT: C 50 LEU cc_start: 0.9502 (tt) cc_final: 0.8848 (mm) REVERT: C 121 MET cc_start: 0.9039 (mmt) cc_final: 0.8643 (mpp) REVERT: C 137 ILE cc_start: 0.8877 (tt) cc_final: 0.8594 (tt) REVERT: C 151 MET cc_start: 0.4862 (ttm) cc_final: 0.4576 (ttm) REVERT: C 209 LYS cc_start: 0.9375 (mtmt) cc_final: 0.8546 (mmtm) REVERT: C 290 PHE cc_start: 0.9414 (m-80) cc_final: 0.9018 (m-80) REVERT: C 309 PHE cc_start: 0.9303 (m-80) cc_final: 0.8910 (m-80) REVERT: C 312 LYS cc_start: 0.9338 (mmpt) cc_final: 0.9031 (mppt) REVERT: C 373 ASP cc_start: 0.8311 (t0) cc_final: 0.7944 (t0) REVERT: C 425 TYR cc_start: 0.4766 (t80) cc_final: 0.4469 (t80) REVERT: C 428 ARG cc_start: 0.5950 (mpt180) cc_final: 0.5281 (mtt180) REVERT: C 462 GLU cc_start: 0.7818 (pt0) cc_final: 0.7520 (pm20) REVERT: C 464 MET cc_start: 0.9566 (tpt) cc_final: 0.9177 (ttm) REVERT: C 523 HIS cc_start: 0.9137 (m-70) cc_final: 0.8784 (m-70) REVERT: C 564 LEU cc_start: 0.8870 (tp) cc_final: 0.8265 (tt) REVERT: C 582 HIS cc_start: 0.9216 (t70) cc_final: 0.8895 (p-80) REVERT: C 627 LEU cc_start: 0.8855 (mm) cc_final: 0.8449 (mp) REVERT: C 666 MET cc_start: 0.9200 (ttm) cc_final: 0.8758 (ptp) REVERT: C 669 PHE cc_start: 0.8606 (m-10) cc_final: 0.8402 (m-80) REVERT: C 764 GLU cc_start: 0.6343 (mp0) cc_final: 0.5928 (mp0) REVERT: C 800 TYR cc_start: 0.9030 (p90) cc_final: 0.8748 (p90) REVERT: C 975 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8505 (tp-100) REVERT: C 977 MET cc_start: 0.9262 (mmm) cc_final: 0.9039 (mmm) REVERT: C 1020 HIS cc_start: 0.9084 (t-90) cc_final: 0.8751 (t-90) REVERT: C 1028 PHE cc_start: 0.8554 (m-80) cc_final: 0.8300 (m-80) REVERT: C 1057 PHE cc_start: 0.8641 (t80) cc_final: 0.8416 (t80) REVERT: C 1074 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8894 (tp-100) REVERT: C 1076 ASP cc_start: 0.8595 (p0) cc_final: 0.8163 (m-30) REVERT: C 1132 TRP cc_start: 0.8755 (t60) cc_final: 0.7904 (t60) REVERT: C 1133 LYS cc_start: 0.9470 (ttmt) cc_final: 0.9209 (tppt) REVERT: C 1150 LEU cc_start: 0.9521 (mm) cc_final: 0.9180 (pp) REVERT: C 1154 PHE cc_start: 0.9226 (m-80) cc_final: 0.8204 (m-80) REVERT: C 1165 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8219 (tm-30) REVERT: C 1214 LEU cc_start: 0.9427 (mt) cc_final: 0.9195 (mt) REVERT: C 1323 TYR cc_start: 0.8461 (t80) cc_final: 0.7929 (t80) REVERT: D 121 MET cc_start: 0.8576 (tpp) cc_final: 0.8154 (tpt) REVERT: D 134 ASP cc_start: 0.8977 (t70) cc_final: 0.8610 (t70) REVERT: D 179 GLN cc_start: 0.8184 (pp30) cc_final: 0.7953 (pp30) REVERT: D 290 PHE cc_start: 0.9147 (m-80) cc_final: 0.8825 (m-80) REVERT: D 291 SER cc_start: 0.8932 (p) cc_final: 0.8528 (t) REVERT: D 360 ARG cc_start: 0.8813 (mpt180) cc_final: 0.8292 (mtt180) REVERT: D 389 ASN cc_start: 0.9061 (m110) cc_final: 0.8860 (m-40) REVERT: D 394 TYR cc_start: 0.7977 (t80) cc_final: 0.7344 (t80) REVERT: D 415 MET cc_start: 0.6934 (pmm) cc_final: 0.5424 (pmm) REVERT: D 461 LEU cc_start: 0.9225 (mp) cc_final: 0.8885 (mm) REVERT: D 496 TYR cc_start: 0.7956 (m-80) cc_final: 0.7688 (m-80) REVERT: D 521 LYS cc_start: 0.8221 (mttt) cc_final: 0.7972 (mttt) REVERT: D 539 ARG cc_start: 0.7788 (ttm170) cc_final: 0.6695 (ttt180) REVERT: D 543 TYR cc_start: 0.8670 (p90) cc_final: 0.8143 (p90) REVERT: D 552 ILE cc_start: 0.9411 (pt) cc_final: 0.9046 (pt) REVERT: D 628 THR cc_start: 0.9144 (p) cc_final: 0.8772 (p) REVERT: D 798 MET cc_start: 0.8230 (mpp) cc_final: 0.7950 (mpp) REVERT: D 870 PHE cc_start: 0.9429 (t80) cc_final: 0.9156 (t80) REVERT: D 965 LEU cc_start: 0.9338 (mt) cc_final: 0.9080 (mt) REVERT: D 985 TYR cc_start: 0.9205 (m-80) cc_final: 0.8868 (m-80) REVERT: D 1067 LEU cc_start: 0.8715 (mt) cc_final: 0.8484 (mt) REVERT: D 1112 ILE cc_start: 0.8615 (mt) cc_final: 0.8359 (mp) REVERT: D 1156 LEU cc_start: 0.7989 (mm) cc_final: 0.7647 (mm) REVERT: D 1165 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8989 (tt0) REVERT: D 1205 GLU cc_start: 0.8429 (pt0) cc_final: 0.8014 (tt0) REVERT: D 1241 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7344 (mp10) REVERT: D 1328 LEU cc_start: 0.9483 (tp) cc_final: 0.8895 (tp) REVERT: D 1330 TYR cc_start: 0.9068 (p90) cc_final: 0.8865 (p90) REVERT: D 1331 ASN cc_start: 0.6293 (m110) cc_final: 0.4213 (m110) outliers start: 6 outliers final: 0 residues processed: 835 average time/residue: 0.2407 time to fit residues: 334.5172 Evaluate side-chains 657 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 655 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 489 optimal weight: 4.9990 chunk 418 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 352 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 444 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** 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** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN B1072 GLN 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 303 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** 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** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.084230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064383 restraints weight = 181662.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066836 restraints weight = 126745.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068766 restraints weight = 95571.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.070297 restraints weight = 75658.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.071503 restraints weight = 62037.653| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41259 Z= 0.212 Angle : 0.819 12.240 56144 Z= 0.414 Chirality : 0.050 0.336 6471 Planarity : 0.006 0.074 7166 Dihedral : 7.903 58.839 6200 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.97 % Rotamer: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.21 % 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: -3.28 (0.11), residues: 5084 helix: -0.14 (0.17), residues: 884 sheet: -2.02 (0.11), residues: 1840 loop : -3.11 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 338 TYR 0.041 0.002 TYR D 316 PHE 0.043 0.002 PHE C1049 TRP 0.039 0.003 TRP D 858 HIS 0.010 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00445 (41179) covalent geometry : angle 0.80240 (55948) SS BOND : bond 0.00846 ( 44) SS BOND : angle 2.34513 ( 88) hydrogen bonds : bond 0.04893 ( 536) hydrogen bonds : angle 5.14646 ( 1608) link_BETA1-4 : bond 0.00894 ( 8) link_BETA1-4 : angle 2.60881 ( 24) link_NAG-ASN : bond 0.00735 ( 28) link_NAG-ASN : angle 3.49258 ( 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 840 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 838 time to evaluate : 1.483 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: A 32 MET cc_start: 0.9482 (ttt) cc_final: 0.9066 (ttm) REVERT: A 38 LEU cc_start: 0.8158 (tt) cc_final: 0.7875 (tt) REVERT: A 50 LEU cc_start: 0.9495 (tt) cc_final: 0.8677 (mm) REVERT: A 121 MET cc_start: 0.9118 (mmt) cc_final: 0.8704 (mpp) REVERT: A 137 ILE cc_start: 0.8895 (tt) cc_final: 0.8658 (tt) REVERT: A 209 LYS cc_start: 0.9381 (mtmt) cc_final: 0.8376 (mmtm) REVERT: A 251 CYS cc_start: 0.8575 (m) cc_final: 0.8181 (t) REVERT: A 290 PHE cc_start: 0.9393 (m-80) cc_final: 0.8998 (m-80) REVERT: A 309 PHE cc_start: 0.9238 (m-80) cc_final: 0.8879 (m-80) REVERT: A 312 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9107 (mptt) REVERT: A 373 ASP cc_start: 0.8398 (t0) cc_final: 0.7959 (t0) REVERT: A 385 PHE cc_start: 0.8888 (m-80) cc_final: 0.8586 (m-80) REVERT: A 428 ARG cc_start: 0.5886 (mpt180) cc_final: 0.5267 (mtt180) REVERT: A 462 GLU cc_start: 0.7735 (pt0) cc_final: 0.7432 (pm20) REVERT: A 523 HIS cc_start: 0.9206 (m-70) cc_final: 0.8884 (m-70) REVERT: A 564 LEU cc_start: 0.8723 (tp) cc_final: 0.8127 (tt) REVERT: A 582 HIS cc_start: 0.9276 (t70) cc_final: 0.8897 (p-80) REVERT: A 627 LEU cc_start: 0.8844 (mm) cc_final: 0.8467 (mp) REVERT: A 666 MET cc_start: 0.9151 (ttm) cc_final: 0.8725 (ptp) REVERT: A 669 PHE cc_start: 0.8510 (m-10) cc_final: 0.8250 (m-10) REVERT: A 688 MET cc_start: 0.8873 (ppp) cc_final: 0.8409 (ppp) REVERT: A 800 TYR cc_start: 0.9052 (p90) cc_final: 0.8773 (p90) REVERT: A 931 LEU cc_start: 0.8840 (tp) cc_final: 0.8393 (tt) REVERT: A 933 LEU cc_start: 0.9222 (mt) cc_final: 0.8930 (mt) REVERT: A 965 LEU cc_start: 0.9268 (tt) cc_final: 0.9038 (tt) REVERT: A 975 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8485 (tp-100) REVERT: A 977 MET cc_start: 0.9337 (mmm) cc_final: 0.9115 (mmm) REVERT: A 983 ASN cc_start: 0.9385 (m-40) cc_final: 0.9091 (m110) REVERT: A 988 ASP cc_start: 0.9180 (m-30) cc_final: 0.8754 (m-30) REVERT: A 1020 HIS cc_start: 0.9027 (t-90) cc_final: 0.8758 (t-90) REVERT: A 1028 PHE cc_start: 0.8536 (m-80) cc_final: 0.8304 (m-10) REVERT: A 1132 TRP cc_start: 0.8708 (t60) cc_final: 0.7885 (t60) REVERT: A 1133 LYS cc_start: 0.9463 (ttmt) cc_final: 0.9209 (tppt) REVERT: A 1150 LEU cc_start: 0.9553 (mm) cc_final: 0.9208 (pp) REVERT: A 1154 PHE cc_start: 0.9322 (m-80) cc_final: 0.8436 (m-80) REVERT: A 1165 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 1214 LEU cc_start: 0.9401 (mt) cc_final: 0.9199 (mt) REVERT: A 1323 TYR cc_start: 0.8393 (t80) cc_final: 0.7756 (t80) REVERT: B 32 MET cc_start: 0.9234 (tpt) cc_final: 0.9021 (tpt) REVERT: B 121 MET cc_start: 0.8691 (tpp) cc_final: 0.8267 (tpt) REVERT: B 290 PHE cc_start: 0.9170 (m-80) cc_final: 0.8810 (m-80) REVERT: B 291 SER cc_start: 0.8983 (p) cc_final: 0.8594 (t) REVERT: B 354 LYS cc_start: 0.8539 (tttp) cc_final: 0.7634 (mttt) REVERT: B 360 ARG cc_start: 0.8654 (mpt180) cc_final: 0.8444 (mpt-90) REVERT: B 389 ASN cc_start: 0.8968 (m110) cc_final: 0.8753 (m-40) REVERT: B 415 MET cc_start: 0.6674 (pmm) cc_final: 0.4886 (pmm) REVERT: B 496 TYR cc_start: 0.7962 (m-80) cc_final: 0.7599 (m-80) REVERT: B 543 TYR cc_start: 0.8663 (p90) cc_final: 0.8114 (p90) REVERT: B 545 VAL cc_start: 0.8917 (t) cc_final: 0.8315 (t) REVERT: B 550 ASP cc_start: 0.9137 (m-30) cc_final: 0.8924 (m-30) REVERT: B 552 ILE cc_start: 0.9380 (pt) cc_final: 0.9010 (pt) REVERT: B 554 ASP cc_start: 0.7074 (t70) cc_final: 0.6872 (t0) REVERT: B 559 ASP cc_start: 0.8295 (t70) cc_final: 0.8073 (t70) REVERT: B 688 MET cc_start: 0.8265 (ppp) cc_final: 0.8065 (ppp) REVERT: B 737 GLU cc_start: 0.8493 (pm20) cc_final: 0.8271 (pp20) REVERT: B 770 PHE cc_start: 0.9004 (t80) cc_final: 0.8741 (t80) REVERT: B 870 PHE cc_start: 0.9357 (t80) cc_final: 0.9083 (t80) REVERT: B 947 SER cc_start: 0.9447 (m) cc_final: 0.9188 (m) REVERT: B 965 LEU cc_start: 0.9371 (mt) cc_final: 0.9151 (mt) REVERT: B 985 TYR cc_start: 0.9045 (m-80) cc_final: 0.8785 (m-80) REVERT: B 1067 LEU cc_start: 0.8849 (mt) cc_final: 0.8645 (mt) REVERT: B 1072 GLN cc_start: 0.9247 (mt0) cc_final: 0.8566 (tt0) REVERT: B 1154 PHE cc_start: 0.8677 (m-80) cc_final: 0.8450 (m-80) REVERT: B 1156 LEU cc_start: 0.7963 (mm) cc_final: 0.7597 (mm) REVERT: B 1165 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8975 (tt0) REVERT: B 1205 GLU cc_start: 0.8427 (pt0) cc_final: 0.8093 (tt0) REVERT: B 1241 GLN cc_start: 0.7422 (mp-120) cc_final: 0.7197 (mm-40) REVERT: B 1316 VAL cc_start: 0.8753 (t) cc_final: 0.8075 (p) REVERT: B 1330 TYR cc_start: 0.9044 (p90) cc_final: 0.8727 (p90) REVERT: C 32 MET cc_start: 0.9481 (ttt) cc_final: 0.9057 (ttm) REVERT: C 38 LEU cc_start: 0.8155 (tt) cc_final: 0.7878 (tt) REVERT: C 50 LEU cc_start: 0.9502 (tt) cc_final: 0.8675 (mm) REVERT: C 121 MET cc_start: 0.9107 (mmt) cc_final: 0.8693 (mpp) REVERT: C 137 ILE cc_start: 0.8877 (tt) cc_final: 0.8663 (tt) REVERT: C 151 MET cc_start: 0.5078 (ttm) cc_final: 0.4763 (ttm) REVERT: C 209 LYS cc_start: 0.9348 (mtmt) cc_final: 0.8267 (mmtm) REVERT: C 289 LYS cc_start: 0.9451 (mppt) cc_final: 0.9214 (mmmt) REVERT: C 290 PHE cc_start: 0.9377 (m-80) cc_final: 0.9033 (m-80) REVERT: C 309 PHE cc_start: 0.9247 (m-80) cc_final: 0.8975 (m-80) REVERT: C 312 LYS cc_start: 0.9252 (mmpt) cc_final: 0.8981 (mmtm) REVERT: C 373 ASP cc_start: 0.8425 (t0) cc_final: 0.8068 (t0) REVERT: C 428 ARG cc_start: 0.5838 (mpt180) cc_final: 0.5222 (mtt180) REVERT: C 462 GLU cc_start: 0.7775 (pt0) cc_final: 0.7487 (pm20) REVERT: C 523 HIS cc_start: 0.9208 (m-70) cc_final: 0.8888 (m-70) REVERT: C 564 LEU cc_start: 0.8712 (tp) cc_final: 0.8113 (tt) REVERT: C 582 HIS cc_start: 0.9267 (t70) cc_final: 0.8892 (p-80) REVERT: C 627 LEU cc_start: 0.8847 (mm) cc_final: 0.8479 (mp) REVERT: C 666 MET cc_start: 0.9163 (ttm) cc_final: 0.8731 (ptp) REVERT: C 669 PHE cc_start: 0.8509 (m-10) cc_final: 0.8251 (m-10) REVERT: C 800 TYR cc_start: 0.8993 (p90) cc_final: 0.8725 (p90) REVERT: C 931 LEU cc_start: 0.8959 (tp) cc_final: 0.8457 (tt) REVERT: C 933 LEU cc_start: 0.9233 (mt) cc_final: 0.8929 (mt) REVERT: C 975 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8495 (tp-100) REVERT: C 1020 HIS cc_start: 0.9013 (t-90) cc_final: 0.8737 (t-90) REVERT: C 1028 PHE cc_start: 0.8573 (m-80) cc_final: 0.8338 (m-10) REVERT: C 1057 PHE cc_start: 0.8696 (t80) cc_final: 0.8449 (t80) REVERT: C 1132 TRP cc_start: 0.8680 (t60) cc_final: 0.7877 (t60) REVERT: C 1133 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9178 (tppt) REVERT: C 1150 LEU cc_start: 0.9549 (mm) cc_final: 0.9187 (pp) REVERT: C 1154 PHE cc_start: 0.9318 (m-80) cc_final: 0.8406 (m-80) REVERT: C 1165 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8250 (tm-30) REVERT: C 1214 LEU cc_start: 0.9401 (mt) cc_final: 0.9194 (mt) REVERT: C 1323 TYR cc_start: 0.8403 (t80) cc_final: 0.7866 (t80) REVERT: D 121 MET cc_start: 0.8696 (tpp) cc_final: 0.8258 (tpt) REVERT: D 151 MET cc_start: 0.6353 (ttp) cc_final: 0.5976 (ttm) REVERT: D 290 PHE cc_start: 0.9158 (m-80) cc_final: 0.8777 (m-80) REVERT: D 291 SER cc_start: 0.8929 (p) cc_final: 0.8527 (t) REVERT: D 354 LYS cc_start: 0.8540 (tttp) cc_final: 0.7641 (mttt) REVERT: D 360 ARG cc_start: 0.8792 (mpt180) cc_final: 0.8186 (mpt-90) REVERT: D 363 ILE cc_start: 0.9312 (tp) cc_final: 0.8793 (tp) REVERT: D 389 ASN cc_start: 0.8965 (m110) cc_final: 0.8745 (m-40) REVERT: D 415 MET cc_start: 0.6682 (pmm) cc_final: 0.4883 (pmm) REVERT: D 461 LEU cc_start: 0.9168 (mp) cc_final: 0.8882 (mm) REVERT: D 496 TYR cc_start: 0.7950 (m-80) cc_final: 0.7562 (m-80) REVERT: D 543 TYR cc_start: 0.8687 (p90) cc_final: 0.8116 (p90) REVERT: D 545 VAL cc_start: 0.8914 (t) cc_final: 0.8315 (t) REVERT: D 550 ASP cc_start: 0.9137 (m-30) cc_final: 0.8919 (m-30) REVERT: D 552 ILE cc_start: 0.9395 (pt) cc_final: 0.9050 (pt) REVERT: D 559 ASP cc_start: 0.8293 (t70) cc_final: 0.8067 (t70) REVERT: D 572 PHE cc_start: 0.8371 (p90) cc_final: 0.8139 (p90) REVERT: D 673 MET cc_start: 0.9190 (tpt) cc_final: 0.8954 (tpp) REVERT: D 737 GLU cc_start: 0.8501 (pm20) cc_final: 0.8279 (pp20) REVERT: D 798 MET cc_start: 0.8117 (mpp) cc_final: 0.7903 (mpp) REVERT: D 870 PHE cc_start: 0.9390 (t80) cc_final: 0.9097 (t80) REVERT: D 985 TYR cc_start: 0.9158 (m-80) cc_final: 0.8874 (m-80) REVERT: D 1067 LEU cc_start: 0.8859 (mt) cc_final: 0.8653 (mt) REVERT: D 1126 PHE cc_start: 0.8873 (m-10) cc_final: 0.8672 (m-10) REVERT: D 1154 PHE cc_start: 0.8684 (m-80) cc_final: 0.8456 (m-80) REVERT: D 1156 LEU cc_start: 0.7965 (mm) cc_final: 0.7598 (mm) REVERT: D 1165 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8971 (tt0) REVERT: D 1205 GLU cc_start: 0.8428 (pt0) cc_final: 0.8101 (tt0) REVERT: D 1241 GLN cc_start: 0.7414 (mp-120) cc_final: 0.7207 (mm-40) REVERT: D 1316 VAL cc_start: 0.8486 (t) cc_final: 0.8182 (p) REVERT: D 1328 LEU cc_start: 0.9488 (tp) cc_final: 0.8926 (tp) REVERT: D 1330 TYR cc_start: 0.9128 (p90) cc_final: 0.8756 (p90) outliers start: 2 outliers final: 0 residues processed: 840 average time/residue: 0.2324 time to fit residues: 325.5378 Evaluate side-chains 669 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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: 0.8980 chunk 377 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 146 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 392 optimal weight: 2.9990 chunk 302 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 441 HIS ** 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** ** 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 477 GLN B 479 HIS B 816 ASN ** B 827 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 200 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 321 HIS ** 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 ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1062 HIS D1089 ASN D1242 GLN ** 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 = 0.3725 r_free = 0.3725 target = 0.087013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066440 restraints weight = 172538.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069047 restraints weight = 119208.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.071117 restraints weight = 89247.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072750 restraints weight = 70264.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.073968 restraints weight = 57512.223| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41259 Z= 0.150 Angle : 0.788 12.083 56144 Z= 0.390 Chirality : 0.050 0.417 6471 Planarity : 0.006 0.066 7166 Dihedral : 7.619 59.015 6200 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.78 % Favored : 89.18 % Rotamer: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.14 % 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: -2.98 (0.11), residues: 5084 helix: 0.12 (0.17), residues: 882 sheet: -1.75 (0.12), residues: 1812 loop : -3.00 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 945 TYR 0.027 0.002 TYR B1152 PHE 0.049 0.002 PHE C1049 TRP 0.057 0.004 TRP D 858 HIS 0.009 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00329 (41179) covalent geometry : angle 0.76916 (55948) SS BOND : bond 0.00980 ( 44) SS BOND : angle 2.13831 ( 88) hydrogen bonds : bond 0.04764 ( 536) hydrogen bonds : angle 5.04624 ( 1608) link_BETA1-4 : bond 0.00849 ( 8) link_BETA1-4 : angle 2.43188 ( 24) link_NAG-ASN : bond 0.00705 ( 28) link_NAG-ASN : angle 3.76653 ( 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 851 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 849 time to evaluate : 1.609 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: 0.9419 (ttt) cc_final: 0.8868 (ttm) REVERT: A 121 MET cc_start: 0.9078 (mmt) cc_final: 0.8832 (mmp) REVERT: A 137 ILE cc_start: 0.8796 (tt) cc_final: 0.8568 (tt) REVERT: A 151 MET cc_start: 0.4531 (ttm) cc_final: 0.4317 (ttm) REVERT: A 209 LYS cc_start: 0.9223 (mtmt) cc_final: 0.9020 (ptmt) REVERT: A 251 CYS cc_start: 0.8423 (m) cc_final: 0.8030 (t) REVERT: A 290 PHE cc_start: 0.9417 (m-80) cc_final: 0.9075 (m-80) REVERT: A 309 PHE cc_start: 0.9106 (m-80) cc_final: 0.8709 (m-80) REVERT: A 312 LYS cc_start: 0.9342 (mmpt) cc_final: 0.9079 (mmtm) REVERT: A 373 ASP cc_start: 0.8400 (t0) cc_final: 0.7994 (t0) REVERT: A 425 TYR cc_start: 0.5102 (t80) cc_final: 0.4775 (t80) REVERT: A 428 ARG cc_start: 0.5841 (mpt180) cc_final: 0.5231 (mtt180) REVERT: A 462 GLU cc_start: 0.7684 (pt0) cc_final: 0.7429 (pm20) REVERT: A 523 HIS cc_start: 0.9251 (m-70) cc_final: 0.8942 (m-70) REVERT: A 564 LEU cc_start: 0.8577 (tp) cc_final: 0.7982 (tt) REVERT: A 582 HIS cc_start: 0.9267 (t70) cc_final: 0.8865 (p-80) REVERT: A 626 ASP cc_start: 0.8946 (p0) cc_final: 0.8289 (t0) REVERT: A 627 LEU cc_start: 0.8797 (mm) cc_final: 0.8446 (mt) REVERT: A 666 MET cc_start: 0.9009 (ttm) cc_final: 0.8659 (ptp) REVERT: A 669 PHE cc_start: 0.8449 (m-10) cc_final: 0.8139 (m-10) REVERT: A 688 MET cc_start: 0.8839 (ppp) cc_final: 0.8424 (ppp) REVERT: A 800 TYR cc_start: 0.8990 (p90) cc_final: 0.8747 (p90) REVERT: A 931 LEU cc_start: 0.8962 (tp) cc_final: 0.8365 (tt) REVERT: A 933 LEU cc_start: 0.9269 (mt) cc_final: 0.8918 (mt) REVERT: A 951 LEU cc_start: 0.8212 (tt) cc_final: 0.8003 (tt) REVERT: A 965 LEU cc_start: 0.9255 (tt) cc_final: 0.9018 (tt) REVERT: A 975 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8414 (tp-100) REVERT: A 977 MET cc_start: 0.9304 (mmm) cc_final: 0.9089 (mmm) REVERT: A 983 ASN cc_start: 0.9414 (m-40) cc_final: 0.8974 (m110) REVERT: A 1020 HIS cc_start: 0.8938 (t-90) cc_final: 0.8641 (t-90) REVERT: A 1028 PHE cc_start: 0.8491 (m-80) cc_final: 0.8265 (m-10) REVERT: A 1112 ILE cc_start: 0.8532 (mt) cc_final: 0.8329 (mt) REVERT: A 1132 TRP cc_start: 0.8917 (t60) cc_final: 0.8583 (t60) REVERT: A 1133 LYS cc_start: 0.9491 (ttmt) cc_final: 0.9159 (tppt) REVERT: A 1150 LEU cc_start: 0.9518 (mm) cc_final: 0.9219 (pp) REVERT: A 1154 PHE cc_start: 0.9304 (m-80) cc_final: 0.8480 (m-80) REVERT: A 1314 MET cc_start: 0.9160 (ptp) cc_final: 0.8936 (ptp) REVERT: B 32 MET cc_start: 0.9177 (tpt) cc_final: 0.8942 (tpt) REVERT: B 121 MET cc_start: 0.8698 (tpp) cc_final: 0.8283 (tpt) REVERT: B 290 PHE cc_start: 0.9101 (m-80) cc_final: 0.8797 (m-80) REVERT: B 291 SER cc_start: 0.8936 (p) cc_final: 0.8528 (t) REVERT: B 310 GLN cc_start: 0.8871 (mp10) cc_final: 0.8670 (mp10) REVERT: B 389 ASN cc_start: 0.8795 (m110) cc_final: 0.8556 (m-40) REVERT: B 415 MET cc_start: 0.6829 (pmm) cc_final: 0.5100 (pmm) REVERT: B 496 TYR cc_start: 0.7862 (m-80) cc_final: 0.7546 (m-80) REVERT: B 539 ARG cc_start: 0.7519 (ttm170) cc_final: 0.6376 (ttt180) REVERT: B 543 TYR cc_start: 0.8614 (p90) cc_final: 0.8073 (p90) REVERT: B 545 VAL cc_start: 0.8820 (t) cc_final: 0.8283 (t) REVERT: B 550 ASP cc_start: 0.9106 (m-30) cc_final: 0.8896 (m-30) REVERT: B 552 ILE cc_start: 0.9379 (pt) cc_final: 0.9078 (pt) REVERT: B 554 ASP cc_start: 0.6854 (t70) cc_final: 0.6590 (t0) REVERT: B 572 PHE cc_start: 0.8180 (p90) cc_final: 0.7951 (p90) REVERT: B 628 THR cc_start: 0.9080 (p) cc_final: 0.8787 (p) REVERT: B 650 ILE cc_start: 0.7079 (mm) cc_final: 0.6857 (mm) REVERT: B 688 MET cc_start: 0.8268 (ppp) cc_final: 0.8039 (ppp) REVERT: B 770 PHE cc_start: 0.8947 (t80) cc_final: 0.8718 (t80) REVERT: B 870 PHE cc_start: 0.9243 (t80) cc_final: 0.9018 (t80) REVERT: B 968 MET cc_start: 0.8487 (tpt) cc_final: 0.8259 (tpt) REVERT: B 985 TYR cc_start: 0.9047 (m-80) cc_final: 0.8797 (m-80) REVERT: B 1165 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8919 (tt0) REVERT: B 1205 GLU cc_start: 0.8443 (pt0) cc_final: 0.8107 (tt0) REVERT: B 1241 GLN cc_start: 0.7559 (mp-120) cc_final: 0.7265 (mp-120) REVERT: B 1316 VAL cc_start: 0.8351 (t) cc_final: 0.8061 (p) REVERT: C 32 MET cc_start: 0.9457 (ttt) cc_final: 0.8926 (ttm) REVERT: C 121 MET cc_start: 0.9107 (mmt) cc_final: 0.8816 (mmp) REVERT: C 131 VAL cc_start: 0.9233 (t) cc_final: 0.8846 (t) REVERT: C 137 ILE cc_start: 0.8712 (tt) cc_final: 0.8457 (tt) REVERT: C 151 MET cc_start: 0.4968 (ttm) cc_final: 0.4161 (ttm) REVERT: C 209 LYS cc_start: 0.9209 (mtmt) cc_final: 0.8438 (mmtm) REVERT: C 251 CYS cc_start: 0.8411 (m) cc_final: 0.8059 (t) REVERT: C 290 PHE cc_start: 0.9445 (m-80) cc_final: 0.9088 (m-80) REVERT: C 309 PHE cc_start: 0.9073 (m-80) cc_final: 0.8670 (m-80) REVERT: C 312 LYS cc_start: 0.9202 (mmpt) cc_final: 0.8932 (mmtm) REVERT: C 318 MET cc_start: 0.8414 (tpp) cc_final: 0.7919 (tpp) REVERT: C 373 ASP cc_start: 0.8382 (t0) cc_final: 0.8052 (t0) REVERT: C 385 PHE cc_start: 0.8812 (m-80) cc_final: 0.8532 (m-80) REVERT: C 425 TYR cc_start: 0.5122 (t80) cc_final: 0.4810 (t80) REVERT: C 428 ARG cc_start: 0.5803 (mpt180) cc_final: 0.5156 (mtt180) REVERT: C 462 GLU cc_start: 0.7694 (pt0) cc_final: 0.7439 (pm20) REVERT: C 523 HIS cc_start: 0.9250 (m-70) cc_final: 0.8943 (m-70) REVERT: C 564 LEU cc_start: 0.8611 (tp) cc_final: 0.8008 (tt) REVERT: C 582 HIS cc_start: 0.9280 (t70) cc_final: 0.8871 (p-80) REVERT: C 626 ASP cc_start: 0.8965 (p0) cc_final: 0.8287 (t0) REVERT: C 627 LEU cc_start: 0.8788 (mm) cc_final: 0.8419 (mt) REVERT: C 666 MET cc_start: 0.9018 (ttm) cc_final: 0.8624 (ptp) REVERT: C 669 PHE cc_start: 0.8443 (m-10) cc_final: 0.8134 (m-10) REVERT: C 688 MET cc_start: 0.8832 (ppp) cc_final: 0.8417 (ppp) REVERT: C 800 TYR cc_start: 0.8909 (p90) cc_final: 0.8645 (p90) REVERT: C 931 LEU cc_start: 0.8908 (tp) cc_final: 0.8321 (tt) REVERT: C 933 LEU cc_start: 0.9230 (mt) cc_final: 0.8860 (mt) REVERT: C 965 LEU cc_start: 0.9223 (tt) cc_final: 0.8947 (tt) REVERT: C 975 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8460 (tp-100) REVERT: C 977 MET cc_start: 0.9328 (mmm) cc_final: 0.9119 (mmm) REVERT: C 983 ASN cc_start: 0.9364 (m-40) cc_final: 0.8940 (m110) REVERT: C 1020 HIS cc_start: 0.8978 (t-90) cc_final: 0.8683 (t-90) REVERT: C 1028 PHE cc_start: 0.8512 (m-80) cc_final: 0.8277 (m-10) REVERT: C 1057 PHE cc_start: 0.8618 (t80) cc_final: 0.8272 (t80) REVERT: C 1132 TRP cc_start: 0.8926 (t60) cc_final: 0.8613 (t60) REVERT: C 1133 LYS cc_start: 0.9478 (ttmt) cc_final: 0.9138 (tppt) REVERT: C 1150 LEU cc_start: 0.9530 (mm) cc_final: 0.9216 (pp) REVERT: C 1154 PHE cc_start: 0.9313 (m-80) cc_final: 0.8468 (m-80) REVERT: C 1314 MET cc_start: 0.9135 (ptp) cc_final: 0.8899 (ptp) REVERT: D 32 MET cc_start: 0.9198 (tpt) cc_final: 0.8985 (tpt) REVERT: D 121 MET cc_start: 0.8688 (tpp) cc_final: 0.8235 (tpt) REVERT: D 151 MET cc_start: 0.6385 (ttp) cc_final: 0.6060 (ttm) REVERT: D 291 SER cc_start: 0.8942 (p) cc_final: 0.8535 (t) REVERT: D 354 LYS cc_start: 0.8516 (tttp) cc_final: 0.7600 (mttt) REVERT: D 389 ASN cc_start: 0.8778 (m110) cc_final: 0.8536 (m-40) REVERT: D 415 MET cc_start: 0.6816 (pmm) cc_final: 0.5078 (pmm) REVERT: D 496 TYR cc_start: 0.7878 (m-80) cc_final: 0.7538 (m-80) REVERT: D 543 TYR cc_start: 0.8636 (p90) cc_final: 0.8047 (p90) REVERT: D 545 VAL cc_start: 0.8811 (t) cc_final: 0.8282 (t) REVERT: D 550 ASP cc_start: 0.9100 (m-30) cc_final: 0.8886 (m-30) REVERT: D 552 ILE cc_start: 0.9390 (pt) cc_final: 0.9092 (pt) REVERT: D 559 ASP cc_start: 0.8297 (t70) cc_final: 0.8092 (t0) REVERT: D 650 ILE cc_start: 0.7079 (mm) cc_final: 0.6859 (mm) REVERT: D 671 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9146 (mt-10) REVERT: D 688 MET cc_start: 0.8264 (ppp) cc_final: 0.7879 (ppp) REVERT: D 870 PHE cc_start: 0.9296 (t80) cc_final: 0.9032 (t80) REVERT: D 968 MET cc_start: 0.8469 (tpt) cc_final: 0.8237 (tpt) REVERT: D 985 TYR cc_start: 0.9066 (m-80) cc_final: 0.8756 (m-80) REVERT: D 1165 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8913 (tt0) REVERT: D 1205 GLU cc_start: 0.8444 (pt0) cc_final: 0.8118 (tt0) REVERT: D 1241 GLN cc_start: 0.7601 (mp-120) cc_final: 0.7295 (mp-120) REVERT: D 1316 VAL cc_start: 0.8273 (t) cc_final: 0.7943 (p) REVERT: D 1328 LEU cc_start: 0.9493 (tp) cc_final: 0.8912 (tp) REVERT: D 1330 TYR cc_start: 0.9041 (p90) cc_final: 0.8818 (p90) outliers start: 2 outliers final: 0 residues processed: 851 average time/residue: 0.2336 time to fit residues: 332.4663 Evaluate side-chains 680 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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: 8.9990 chunk 455 optimal weight: 4.9990 chunk 501 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 504 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 355 optimal weight: 3.9990 chunk 364 optimal weight: 0.7980 chunk 372 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** 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** ** 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 232 GLN ** B 321 HIS ** 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 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 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** B1331 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 HIS ** 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 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064538 restraints weight = 177734.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066995 restraints weight = 123874.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068925 restraints weight = 93386.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070460 restraints weight = 73911.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071648 restraints weight = 60673.266| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6776 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= 0.190 Angle : 0.802 12.189 56144 Z= 0.404 Chirality : 0.050 0.363 6471 Planarity : 0.006 0.183 7166 Dihedral : 7.684 59.490 6200 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.01 % Favored : 88.91 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.10 % 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: -3.05 (0.11), residues: 5084 helix: 0.03 (0.17), residues: 886 sheet: -1.84 (0.12), residues: 1836 loop : -3.01 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 823 TYR 0.025 0.002 TYR B1152 PHE 0.045 0.002 PHE A1049 TRP 0.033 0.003 TRP D 436 HIS 0.008 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00405 (41179) covalent geometry : angle 0.78447 (55948) SS BOND : bond 0.00594 ( 44) SS BOND : angle 2.28946 ( 88) hydrogen bonds : bond 0.04949 ( 536) hydrogen bonds : angle 5.26170 ( 1608) link_BETA1-4 : bond 0.00779 ( 8) link_BETA1-4 : angle 2.55583 ( 24) link_NAG-ASN : bond 0.00689 ( 28) link_NAG-ASN : angle 3.54889 ( 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 825 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 823 time to evaluate : 1.688 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: A 32 MET cc_start: 0.9439 (ttt) cc_final: 0.9044 (ttt) REVERT: A 38 LEU cc_start: 0.8118 (tt) cc_final: 0.7759 (tt) REVERT: A 121 MET cc_start: 0.9074 (mmt) cc_final: 0.8695 (mpp) REVERT: A 137 ILE cc_start: 0.8794 (tt) cc_final: 0.8573 (tt) REVERT: A 151 MET cc_start: 0.4718 (ttm) cc_final: 0.4039 (ttt) REVERT: A 251 CYS cc_start: 0.8356 (m) cc_final: 0.7997 (t) REVERT: A 290 PHE cc_start: 0.9402 (m-80) cc_final: 0.9067 (m-80) REVERT: A 309 PHE cc_start: 0.9074 (m-80) cc_final: 0.8598 (m-80) REVERT: A 373 ASP cc_start: 0.8425 (t0) cc_final: 0.8196 (t0) REVERT: A 385 PHE cc_start: 0.8835 (m-80) cc_final: 0.8506 (m-80) REVERT: A 415 MET cc_start: 0.6131 (ppp) cc_final: 0.5829 (ppp) REVERT: A 425 TYR cc_start: 0.5141 (t80) cc_final: 0.4819 (t80) REVERT: A 428 ARG cc_start: 0.6068 (mpt180) cc_final: 0.5347 (mtt180) REVERT: A 462 GLU cc_start: 0.7738 (pt0) cc_final: 0.7512 (pm20) REVERT: A 491 LYS cc_start: 0.9377 (mmpt) cc_final: 0.9102 (mmmt) REVERT: A 523 HIS cc_start: 0.9225 (m-70) cc_final: 0.8903 (m-70) REVERT: A 564 LEU cc_start: 0.8699 (tp) cc_final: 0.7874 (tt) REVERT: A 582 HIS cc_start: 0.9238 (t70) cc_final: 0.8867 (p-80) REVERT: A 626 ASP cc_start: 0.8938 (p0) cc_final: 0.8343 (t0) REVERT: A 666 MET cc_start: 0.8994 (ttm) cc_final: 0.8579 (ptp) REVERT: A 669 PHE cc_start: 0.8441 (m-10) cc_final: 0.8190 (m-10) REVERT: A 800 TYR cc_start: 0.9017 (p90) cc_final: 0.8705 (p90) REVERT: A 931 LEU cc_start: 0.8837 (tp) cc_final: 0.8285 (tt) REVERT: A 933 LEU cc_start: 0.9213 (mt) cc_final: 0.8856 (mt) REVERT: A 965 LEU cc_start: 0.9288 (tt) cc_final: 0.9071 (tt) REVERT: A 975 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8521 (tp-100) REVERT: A 977 MET cc_start: 0.9307 (mmm) cc_final: 0.9085 (mmm) REVERT: A 983 ASN cc_start: 0.9374 (m-40) cc_final: 0.8972 (m110) REVERT: A 1020 HIS cc_start: 0.8952 (t-90) cc_final: 0.8666 (t-90) REVERT: A 1028 PHE cc_start: 0.8503 (m-80) cc_final: 0.8270 (m-10) REVERT: A 1132 TRP cc_start: 0.8906 (t60) cc_final: 0.8481 (t60) REVERT: A 1133 LYS cc_start: 0.9493 (ttmt) cc_final: 0.9171 (tppt) REVERT: A 1144 VAL cc_start: 0.8377 (p) cc_final: 0.7976 (m) REVERT: A 1150 LEU cc_start: 0.9543 (mm) cc_final: 0.9183 (pp) REVERT: A 1154 PHE cc_start: 0.9320 (m-80) cc_final: 0.8453 (m-80) REVERT: A 1323 TYR cc_start: 0.7997 (t80) cc_final: 0.6789 (t80) REVERT: B 113 GLU cc_start: 0.8711 (tp30) cc_final: 0.8478 (tp30) REVERT: B 121 MET cc_start: 0.8645 (tpp) cc_final: 0.8280 (tpt) REVERT: B 290 PHE cc_start: 0.9046 (m-80) cc_final: 0.8819 (m-80) REVERT: B 360 ARG cc_start: 0.8422 (mpt180) cc_final: 0.7875 (mtt180) REVERT: B 389 ASN cc_start: 0.8926 (m110) cc_final: 0.8689 (m-40) REVERT: B 415 MET cc_start: 0.6991 (pmm) cc_final: 0.5287 (pmm) REVERT: B 422 ARG cc_start: 0.9136 (mtt90) cc_final: 0.8402 (mtm-85) REVERT: B 539 ARG cc_start: 0.7604 (ttm170) cc_final: 0.6815 (ttt180) REVERT: B 543 TYR cc_start: 0.8535 (p90) cc_final: 0.8226 (p90) REVERT: B 552 ILE cc_start: 0.9389 (pt) cc_final: 0.8914 (pt) REVERT: B 554 ASP cc_start: 0.7244 (t70) cc_final: 0.7007 (t70) REVERT: B 559 ASP cc_start: 0.8375 (t70) cc_final: 0.8173 (t70) REVERT: B 650 ILE cc_start: 0.7071 (mm) cc_final: 0.6862 (mm) REVERT: B 770 PHE cc_start: 0.8893 (t80) cc_final: 0.8611 (t80) REVERT: B 870 PHE cc_start: 0.9248 (t80) cc_final: 0.9014 (t80) REVERT: B 985 TYR cc_start: 0.9100 (m-80) cc_final: 0.8883 (m-80) REVERT: B 1165 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8978 (tt0) REVERT: B 1205 GLU cc_start: 0.8491 (pt0) cc_final: 0.8188 (tt0) REVERT: B 1316 VAL cc_start: 0.8648 (t) cc_final: 0.8376 (p) REVERT: C 32 MET cc_start: 0.9454 (ttt) cc_final: 0.9085 (ttt) REVERT: C 38 LEU cc_start: 0.8106 (tt) cc_final: 0.7754 (tt) REVERT: C 121 MET cc_start: 0.9093 (mmt) cc_final: 0.8700 (mpp) REVERT: C 131 VAL cc_start: 0.9299 (t) cc_final: 0.8880 (t) REVERT: C 137 ILE cc_start: 0.8771 (tt) cc_final: 0.8544 (tt) REVERT: C 151 MET cc_start: 0.5151 (ttm) cc_final: 0.4092 (ttm) REVERT: C 251 CYS cc_start: 0.8325 (m) cc_final: 0.8017 (t) REVERT: C 289 LYS cc_start: 0.9409 (mppt) cc_final: 0.9188 (mmmt) REVERT: C 290 PHE cc_start: 0.9448 (m-80) cc_final: 0.9148 (m-80) REVERT: C 309 PHE cc_start: 0.9067 (m-80) cc_final: 0.8550 (m-80) REVERT: C 373 ASP cc_start: 0.8422 (t0) cc_final: 0.8200 (t0) REVERT: C 385 PHE cc_start: 0.8825 (m-80) cc_final: 0.8541 (m-80) REVERT: C 415 MET cc_start: 0.6092 (ppp) cc_final: 0.5800 (ppp) REVERT: C 425 TYR cc_start: 0.5147 (t80) cc_final: 0.4817 (t80) REVERT: C 428 ARG cc_start: 0.5937 (mpt180) cc_final: 0.5276 (mtt180) REVERT: C 462 GLU cc_start: 0.7739 (pt0) cc_final: 0.7516 (pm20) REVERT: C 491 LYS cc_start: 0.9380 (mmpt) cc_final: 0.9108 (mmmt) REVERT: C 523 HIS cc_start: 0.9223 (m-70) cc_final: 0.8901 (m-70) REVERT: C 564 LEU cc_start: 0.8643 (tp) cc_final: 0.8015 (tt) REVERT: C 582 HIS cc_start: 0.9251 (t70) cc_final: 0.8868 (p-80) REVERT: C 626 ASP cc_start: 0.8964 (p0) cc_final: 0.8343 (t0) REVERT: C 666 MET cc_start: 0.9039 (ttm) cc_final: 0.8615 (ptp) REVERT: C 669 PHE cc_start: 0.8437 (m-10) cc_final: 0.8190 (m-10) REVERT: C 800 TYR cc_start: 0.8962 (p90) cc_final: 0.8674 (p90) REVERT: C 931 LEU cc_start: 0.8923 (tp) cc_final: 0.8438 (tt) REVERT: C 933 LEU cc_start: 0.9210 (mt) cc_final: 0.8913 (mt) REVERT: C 965 LEU cc_start: 0.9255 (tt) cc_final: 0.9019 (tt) REVERT: C 975 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8494 (tp-100) REVERT: C 977 MET cc_start: 0.9307 (mmm) cc_final: 0.9078 (mmm) REVERT: C 983 ASN cc_start: 0.9426 (m-40) cc_final: 0.9039 (m110) REVERT: C 988 ASP cc_start: 0.9245 (m-30) cc_final: 0.8999 (m-30) REVERT: C 1020 HIS cc_start: 0.8953 (t-90) cc_final: 0.8665 (t-90) REVERT: C 1028 PHE cc_start: 0.8526 (m-80) cc_final: 0.8281 (m-10) REVERT: C 1057 PHE cc_start: 0.8615 (t80) cc_final: 0.8368 (t80) REVERT: C 1132 TRP cc_start: 0.8920 (t60) cc_final: 0.8505 (t60) REVERT: C 1133 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9165 (tppt) REVERT: C 1144 VAL cc_start: 0.8399 (p) cc_final: 0.7987 (m) REVERT: C 1150 LEU cc_start: 0.9543 (mm) cc_final: 0.9158 (pp) REVERT: C 1154 PHE cc_start: 0.9289 (m-80) cc_final: 0.8447 (m-80) REVERT: C 1323 TYR cc_start: 0.8214 (t80) cc_final: 0.7278 (t80) REVERT: C 1324 LEU cc_start: 0.8324 (mp) cc_final: 0.8040 (tt) REVERT: D 113 GLU cc_start: 0.8705 (tp30) cc_final: 0.8446 (tp30) REVERT: D 121 MET cc_start: 0.8638 (tpp) cc_final: 0.8263 (tpt) REVERT: D 151 MET cc_start: 0.6422 (ttp) cc_final: 0.5994 (ttm) REVERT: D 360 ARG cc_start: 0.8487 (mpt180) cc_final: 0.8096 (mtt180) REVERT: D 389 ASN cc_start: 0.8970 (m110) cc_final: 0.8731 (m-40) REVERT: D 415 MET cc_start: 0.7023 (pmm) cc_final: 0.5300 (pmm) REVERT: D 421 VAL cc_start: 0.9601 (t) cc_final: 0.9395 (t) REVERT: D 422 ARG cc_start: 0.9125 (mtt90) cc_final: 0.8375 (mtm-85) REVERT: D 550 ASP cc_start: 0.9056 (m-30) cc_final: 0.8830 (m-30) REVERT: D 552 ILE cc_start: 0.9395 (pt) cc_final: 0.8982 (pt) REVERT: D 554 ASP cc_start: 0.7198 (t0) cc_final: 0.6840 (t0) REVERT: D 559 ASP cc_start: 0.8346 (t70) cc_final: 0.8136 (t70) REVERT: D 572 PHE cc_start: 0.8240 (p90) cc_final: 0.7870 (p90) REVERT: D 650 ILE cc_start: 0.7079 (mm) cc_final: 0.6875 (mm) REVERT: D 798 MET cc_start: 0.8316 (mpp) cc_final: 0.8035 (mpp) REVERT: D 870 PHE cc_start: 0.9307 (t80) cc_final: 0.9039 (t80) REVERT: D 985 TYR cc_start: 0.9126 (m-80) cc_final: 0.8781 (m-80) REVERT: D 1165 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8975 (tt0) REVERT: D 1205 GLU cc_start: 0.8488 (pt0) cc_final: 0.8191 (tt0) REVERT: D 1314 MET cc_start: 0.9065 (mpp) cc_final: 0.8576 (mpp) REVERT: D 1328 LEU cc_start: 0.9468 (tp) cc_final: 0.9086 (tp) REVERT: D 1330 TYR cc_start: 0.9000 (p90) cc_final: 0.8574 (p90) outliers start: 2 outliers final: 0 residues processed: 825 average time/residue: 0.2349 time to fit residues: 322.6865 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 : 1.580 ------------------------------------------------------------------------------- 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: 10.0000 chunk 247 optimal weight: 5.9990 chunk 203 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 GLN B 303 GLN ** B 321 HIS ** 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 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS B1089 ASN B1242 GLN ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 HIS D 477 GLN D 479 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3708 r_free = 0.3708 target = 0.086181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065708 restraints weight = 171888.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068235 restraints weight = 119699.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.070251 restraints weight = 90104.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071862 restraints weight = 71188.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073113 restraints weight = 58371.410| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41259 Z= 0.148 Angle : 0.776 11.936 56144 Z= 0.385 Chirality : 0.050 0.328 6471 Planarity : 0.006 0.074 7166 Dihedral : 7.499 59.315 6200 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.35 % Favored : 89.59 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % 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: 0.20 (0.17), residues: 885 sheet: -1.70 (0.12), residues: 1812 loop : -2.90 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 823 TYR 0.023 0.002 TYR B1152 PHE 0.048 0.002 PHE C1049 TRP 0.038 0.003 TRP D1132 HIS 0.006 0.001 HIS C1195 Details of bonding type rmsd covalent geometry : bond 0.00324 (41179) covalent geometry : angle 0.75858 (55948) SS BOND : bond 0.00540 ( 44) SS BOND : angle 2.28467 ( 88) hydrogen bonds : bond 0.04714 ( 536) hydrogen bonds : angle 5.12043 ( 1608) link_BETA1-4 : bond 0.00819 ( 8) link_BETA1-4 : angle 2.48755 ( 24) link_NAG-ASN : bond 0.00688 ( 28) link_NAG-ASN : angle 3.41345 ( 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 833 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 831 time to evaluate : 1.470 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: A 32 MET cc_start: 0.9463 (ttt) cc_final: 0.9025 (tpp) REVERT: A 121 MET cc_start: 0.9138 (mmt) cc_final: 0.8824 (mmp) REVERT: A 137 ILE cc_start: 0.8799 (tt) cc_final: 0.8567 (tt) REVERT: A 151 MET cc_start: 0.4678 (ttm) cc_final: 0.4079 (ttt) REVERT: A 251 CYS cc_start: 0.8403 (m) cc_final: 0.8012 (t) REVERT: A 290 PHE cc_start: 0.9396 (m-80) cc_final: 0.9062 (m-80) REVERT: A 309 PHE cc_start: 0.9032 (m-80) cc_final: 0.8545 (m-80) REVERT: A 385 PHE cc_start: 0.8783 (m-80) cc_final: 0.8476 (m-80) REVERT: A 415 MET cc_start: 0.5850 (ppp) cc_final: 0.5435 (ppp) REVERT: A 425 TYR cc_start: 0.5116 (t80) cc_final: 0.4855 (t80) REVERT: A 428 ARG cc_start: 0.5956 (mpt180) cc_final: 0.5284 (mtt180) REVERT: A 491 LYS cc_start: 0.9321 (mmpt) cc_final: 0.9099 (mmmt) REVERT: A 523 HIS cc_start: 0.9213 (m-70) cc_final: 0.8906 (m-70) REVERT: A 564 LEU cc_start: 0.8467 (tp) cc_final: 0.7821 (tt) REVERT: A 582 HIS cc_start: 0.9275 (t70) cc_final: 0.8832 (p-80) REVERT: A 626 ASP cc_start: 0.8993 (p0) cc_final: 0.8453 (t0) REVERT: A 666 MET cc_start: 0.9021 (ttm) cc_final: 0.8596 (ptp) REVERT: A 800 TYR cc_start: 0.8998 (p90) cc_final: 0.8704 (p90) REVERT: A 913 GLU cc_start: 0.9206 (pm20) cc_final: 0.8614 (pm20) REVERT: A 931 LEU cc_start: 0.8983 (tp) cc_final: 0.8646 (tp) REVERT: A 933 LEU cc_start: 0.9210 (mt) cc_final: 0.8985 (mt) REVERT: A 965 LEU cc_start: 0.9254 (tt) cc_final: 0.9044 (tt) REVERT: A 975 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8439 (tp-100) REVERT: A 977 MET cc_start: 0.9267 (mmm) cc_final: 0.9057 (mmm) REVERT: A 983 ASN cc_start: 0.9460 (m-40) cc_final: 0.9027 (m110) REVERT: A 988 ASP cc_start: 0.9132 (m-30) cc_final: 0.8824 (m-30) REVERT: A 1020 HIS cc_start: 0.8876 (t-90) cc_final: 0.8575 (t-90) REVERT: A 1028 PHE cc_start: 0.8463 (m-80) cc_final: 0.8228 (m-10) REVERT: A 1112 ILE cc_start: 0.8545 (mt) cc_final: 0.8322 (mt) REVERT: A 1132 TRP cc_start: 0.8818 (t60) cc_final: 0.8180 (t60) REVERT: A 1133 LYS cc_start: 0.9480 (ttmt) cc_final: 0.9203 (tppt) REVERT: A 1144 VAL cc_start: 0.8438 (p) cc_final: 0.8033 (m) REVERT: A 1150 LEU cc_start: 0.9559 (mm) cc_final: 0.9189 (pp) REVERT: A 1154 PHE cc_start: 0.9284 (m-80) cc_final: 0.8379 (m-80) REVERT: A 1214 LEU cc_start: 0.9325 (mt) cc_final: 0.9119 (mt) REVERT: A 1324 LEU cc_start: 0.8275 (tt) cc_final: 0.8044 (mm) REVERT: B 121 MET cc_start: 0.8670 (tpp) cc_final: 0.8291 (tpt) REVERT: B 134 ASP cc_start: 0.9128 (t70) cc_final: 0.7873 (t70) REVERT: B 389 ASN cc_start: 0.8807 (m110) cc_final: 0.8551 (m-40) REVERT: B 415 MET cc_start: 0.7135 (pmm) cc_final: 0.5610 (pmm) REVERT: B 422 ARG cc_start: 0.9136 (mtt90) cc_final: 0.8422 (mtm-85) REVERT: B 479 HIS cc_start: 0.9272 (m90) cc_final: 0.9025 (m90) REVERT: B 500 MET cc_start: 0.4468 (tpt) cc_final: 0.3639 (tpt) REVERT: B 542 ILE cc_start: 0.9507 (mp) cc_final: 0.9238 (tp) REVERT: B 550 ASP cc_start: 0.9194 (t0) cc_final: 0.8929 (t0) REVERT: B 552 ILE cc_start: 0.9368 (pt) cc_final: 0.8927 (pt) REVERT: B 559 ASP cc_start: 0.8417 (t70) cc_final: 0.8195 (t70) REVERT: B 586 ARG cc_start: 0.8914 (ttt90) cc_final: 0.8595 (tpt170) REVERT: B 650 ILE cc_start: 0.7065 (mm) cc_final: 0.6859 (mm) REVERT: B 671 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8928 (mp0) REVERT: B 673 MET cc_start: 0.9081 (tpt) cc_final: 0.8876 (tpp) REVERT: B 770 PHE cc_start: 0.8872 (t80) cc_final: 0.8152 (t80) REVERT: B 870 PHE cc_start: 0.9155 (t80) cc_final: 0.8947 (t80) REVERT: B 985 TYR cc_start: 0.9080 (m-80) cc_final: 0.8879 (m-80) REVERT: B 1067 LEU cc_start: 0.8834 (mt) cc_final: 0.8602 (mt) REVERT: B 1154 PHE cc_start: 0.8614 (m-80) cc_final: 0.7247 (m-80) REVERT: B 1165 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8915 (tt0) REVERT: B 1316 VAL cc_start: 0.8593 (t) cc_final: 0.8288 (p) REVERT: B 1330 TYR cc_start: 0.9038 (p90) cc_final: 0.8405 (p90) REVERT: C 32 MET cc_start: 0.9470 (ttt) cc_final: 0.9019 (tpp) REVERT: C 121 MET cc_start: 0.9145 (mmt) cc_final: 0.8822 (mmp) REVERT: C 131 VAL cc_start: 0.9294 (t) cc_final: 0.8650 (t) REVERT: C 137 ILE cc_start: 0.8766 (tt) cc_final: 0.8532 (tt) REVERT: C 146 PHE cc_start: 0.9251 (p90) cc_final: 0.9009 (p90) REVERT: C 151 MET cc_start: 0.5104 (ttm) cc_final: 0.4094 (ttm) REVERT: C 251 CYS cc_start: 0.8378 (m) cc_final: 0.8047 (t) REVERT: C 290 PHE cc_start: 0.9417 (m-80) cc_final: 0.9071 (m-80) REVERT: C 309 PHE cc_start: 0.8993 (m-80) cc_final: 0.8446 (m-80) REVERT: C 385 PHE cc_start: 0.8791 (m-80) cc_final: 0.8512 (m-80) REVERT: C 415 MET cc_start: 0.5821 (ppp) cc_final: 0.5407 (ppp) REVERT: C 425 TYR cc_start: 0.5071 (t80) cc_final: 0.4811 (t80) REVERT: C 428 ARG cc_start: 0.5892 (mpt180) cc_final: 0.5210 (mtt180) REVERT: C 491 LYS cc_start: 0.9339 (mmpt) cc_final: 0.9119 (mmmt) REVERT: C 523 HIS cc_start: 0.9218 (m-70) cc_final: 0.8912 (m-70) REVERT: C 564 LEU cc_start: 0.8587 (tp) cc_final: 0.7974 (tt) REVERT: C 582 HIS cc_start: 0.9275 (t70) cc_final: 0.8835 (p-80) REVERT: C 626 ASP cc_start: 0.8992 (p0) cc_final: 0.8527 (t0) REVERT: C 666 MET cc_start: 0.9022 (ttm) cc_final: 0.8596 (ptp) REVERT: C 800 TYR cc_start: 0.8852 (p90) cc_final: 0.8570 (p90) REVERT: C 931 LEU cc_start: 0.8915 (tp) cc_final: 0.8323 (tt) REVERT: C 933 LEU cc_start: 0.9214 (mt) cc_final: 0.8841 (mt) REVERT: C 965 LEU cc_start: 0.9225 (tt) cc_final: 0.8971 (tt) REVERT: C 975 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8458 (tp-100) REVERT: C 977 MET cc_start: 0.9286 (mmm) cc_final: 0.9078 (mmm) REVERT: C 983 ASN cc_start: 0.9436 (m-40) cc_final: 0.8973 (m110) REVERT: C 988 ASP cc_start: 0.9279 (m-30) cc_final: 0.9006 (m-30) REVERT: C 1020 HIS cc_start: 0.8882 (t-90) cc_final: 0.8581 (t-90) REVERT: C 1028 PHE cc_start: 0.8488 (m-80) cc_final: 0.8245 (m-10) REVERT: C 1057 PHE cc_start: 0.8689 (t80) cc_final: 0.8426 (t80) REVERT: C 1112 ILE cc_start: 0.8526 (mt) cc_final: 0.8315 (mt) REVERT: C 1132 TRP cc_start: 0.8814 (t60) cc_final: 0.8208 (t60) REVERT: C 1133 LYS cc_start: 0.9455 (ttmt) cc_final: 0.9166 (tppt) REVERT: C 1144 VAL cc_start: 0.8456 (p) cc_final: 0.8044 (m) REVERT: C 1150 LEU cc_start: 0.9565 (mm) cc_final: 0.9198 (pp) REVERT: C 1154 PHE cc_start: 0.9275 (m-80) cc_final: 0.8320 (m-80) REVERT: C 1314 MET cc_start: 0.9100 (ptp) cc_final: 0.8895 (ptp) REVERT: C 1323 TYR cc_start: 0.8164 (t80) cc_final: 0.7221 (t80) REVERT: C 1324 LEU cc_start: 0.8309 (mp) cc_final: 0.8060 (tt) REVERT: D 121 MET cc_start: 0.8667 (tpp) cc_final: 0.8278 (tpt) REVERT: D 134 ASP cc_start: 0.9120 (t70) cc_final: 0.7850 (t70) REVERT: D 151 MET cc_start: 0.6616 (ttp) cc_final: 0.6259 (ttm) REVERT: D 360 ARG cc_start: 0.8447 (mpt180) cc_final: 0.8072 (mtt180) REVERT: D 389 ASN cc_start: 0.8782 (m110) cc_final: 0.8511 (m-40) REVERT: D 415 MET cc_start: 0.7336 (pmm) cc_final: 0.6225 (pmm) REVERT: D 422 ARG cc_start: 0.9134 (mtt90) cc_final: 0.8409 (mtm-85) REVERT: D 479 HIS cc_start: 0.9188 (m-70) cc_final: 0.8962 (m90) REVERT: D 500 MET cc_start: 0.4617 (tpt) cc_final: 0.3819 (tpt) REVERT: D 552 ILE cc_start: 0.9336 (pt) cc_final: 0.8958 (pt) REVERT: D 554 ASP cc_start: 0.7179 (t0) cc_final: 0.6511 (t0) REVERT: D 559 ASP cc_start: 0.8373 (t70) cc_final: 0.8144 (t70) REVERT: D 572 PHE cc_start: 0.8268 (p90) cc_final: 0.7816 (p90) REVERT: D 650 ILE cc_start: 0.7101 (mm) cc_final: 0.6895 (mm) REVERT: D 688 MET cc_start: 0.8209 (ppp) cc_final: 0.7842 (ppp) REVERT: D 770 PHE cc_start: 0.8924 (t80) cc_final: 0.8687 (t80) REVERT: D 786 LEU cc_start: 0.9138 (mp) cc_final: 0.8890 (mp) REVERT: D 870 PHE cc_start: 0.9196 (t80) cc_final: 0.8962 (t80) REVERT: D 985 TYR cc_start: 0.9088 (m-80) cc_final: 0.8771 (m-80) REVERT: D 1044 PHE cc_start: 0.9378 (t80) cc_final: 0.9178 (t80) REVERT: D 1154 PHE cc_start: 0.8619 (m-80) cc_final: 0.7262 (m-80) REVERT: D 1165 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8935 (tt0) REVERT: D 1241 GLN cc_start: 0.7416 (mp-120) cc_final: 0.7132 (mp10) REVERT: D 1330 TYR cc_start: 0.8912 (p90) cc_final: 0.8662 (p90) outliers start: 2 outliers final: 0 residues processed: 833 average time/residue: 0.2352 time to fit residues: 326.2047 Evaluate side-chains 677 residues out of total 4451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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: 10.0000 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 406 optimal weight: 30.0000 chunk 210 optimal weight: 30.0000 chunk 263 optimal weight: 20.0000 chunk 446 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 373 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 523 HIS ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS 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** C 112 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 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** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.080558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061253 restraints weight = 188504.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063508 restraints weight = 131490.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065270 restraints weight = 99360.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066691 restraints weight = 79099.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.067815 restraints weight = 65404.721| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 41259 Z= 0.283 Angle : 0.914 13.632 56144 Z= 0.467 Chirality : 0.053 0.345 6471 Planarity : 0.007 0.092 7166 Dihedral : 7.995 58.620 6200 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 28.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.37 % Favored : 87.55 % Rotamer: Outliers : 0.02 % Allowed : 0.72 % 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: -3.32 (0.11), residues: 5084 helix: -0.28 (0.16), residues: 891 sheet: -2.09 (0.12), residues: 1819 loop : -3.06 (0.11), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 823 TYR 0.032 0.003 TYR D 316 PHE 0.038 0.003 PHE B 155 TRP 0.061 0.006 TRP A1183 HIS 0.010 0.002 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00589 (41179) covalent geometry : angle 0.89790 (55948) SS BOND : bond 0.00926 ( 44) SS BOND : angle 2.48992 ( 88) hydrogen bonds : bond 0.05064 ( 536) hydrogen bonds : angle 5.52883 ( 1608) link_BETA1-4 : bond 0.00765 ( 8) link_BETA1-4 : angle 2.66676 ( 24) link_NAG-ASN : bond 0.00772 ( 28) link_NAG-ASN : angle 3.56648 ( 84) =============================================================================== Job complete usr+sys time: 8249.07 seconds wall clock time: 144 minutes 4.56 seconds (8644.56 seconds total)