Starting phenix.real_space_refine on Sat Mar 7 08:05:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7q_12753/03_2026/7o7q_12753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7q_12753/03_2026/7o7q_12753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o7q_12753/03_2026/7o7q_12753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7q_12753/03_2026/7o7q_12753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7q_12753/03_2026/7o7q_12753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7q_12753/03_2026/7o7q_12753.map" } resolution = 3.6 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 25734 2.51 5 N 6746 2.21 5 O 7878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 239 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: 40530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "B" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "C" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "D" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 8.98, per 1000 atoms: 0.22 Number of scatterers: 40530 At special positions: 0 Unit cell: (214.635, 149.721, 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 7878 8.00 N 6746 7.00 C 25734 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 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=2.03 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=2.04 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 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=2.03 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=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 247 " " NAG D2004 " - " ASN D 396 " " NAG D2005 " - " ASN D 410 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 869 " " NAG L 1 " - " ASN D 991 " Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 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 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: 5.227A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.806A 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 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: 5.227A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.811A 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 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: 5.227A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.806A 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 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: 5.228A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 3.757A 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: 3.811A 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' 540 hydrogen bonds defined for protein. 1620 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: 5.13 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 6721 1.26 - 1.41: 9881 1.41 - 1.55: 24495 1.55 - 1.70: 71 1.70 - 1.84: 252 Bond restraints: 41420 Sorted by residual: bond pdb=" C SER D 949 " pdb=" N VAL D 950 " ideal model delta sigma weight residual 1.330 1.117 0.213 1.42e-02 4.96e+03 2.25e+02 bond pdb=" C SER C 949 " pdb=" N VAL C 950 " ideal model delta sigma weight residual 1.330 1.172 0.159 1.97e-02 2.58e+03 6.48e+01 bond pdb=" C GLN C 168 " pdb=" N ASP C 169 " ideal model delta sigma weight residual 1.329 1.466 -0.138 1.86e-02 2.89e+03 5.47e+01 bond pdb=" C GLN A 168 " pdb=" N ASP A 169 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.86e-02 2.89e+03 5.44e+01 bond pdb=" C GLY B 629 " pdb=" N PHE B 630 " ideal model delta sigma weight residual 1.331 1.241 0.089 1.48e-02 4.57e+03 3.64e+01 ... (remaining 41415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 53820 3.42 - 6.83: 2081 6.83 - 10.25: 288 10.25 - 13.67: 61 13.67 - 17.08: 20 Bond angle restraints: 56270 Sorted by residual: angle pdb=" N MET A 464 " pdb=" CA MET A 464 " pdb=" C MET A 464 " ideal model delta sigma weight residual 110.65 99.13 11.52 1.26e+00 6.30e-01 8.35e+01 angle pdb=" N MET C 464 " pdb=" CA MET C 464 " pdb=" C MET C 464 " ideal model delta sigma weight residual 110.65 99.13 11.52 1.26e+00 6.30e-01 8.35e+01 angle pdb=" N ASN B 154 " pdb=" CA ASN B 154 " pdb=" C ASN B 154 " ideal model delta sigma weight residual 110.48 97.32 13.16 1.48e+00 4.57e-01 7.91e+01 angle pdb=" N ASN D 154 " pdb=" CA ASN D 154 " pdb=" C ASN D 154 " ideal model delta sigma weight residual 110.48 97.37 13.11 1.48e+00 4.57e-01 7.84e+01 angle pdb=" N MET D 464 " pdb=" CA MET D 464 " pdb=" C MET D 464 " ideal model delta sigma weight residual 110.65 99.92 10.73 1.26e+00 6.30e-01 7.25e+01 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 23483 21.51 - 43.01: 1676 43.01 - 64.52: 313 64.52 - 86.02: 66 86.02 - 107.53: 24 Dihedral angle restraints: 25562 sinusoidal: 10648 harmonic: 14914 Sorted by residual: dihedral pdb=" CB CYS D1079 " pdb=" SG CYS D1079 " pdb=" SG CYS D1127 " pdb=" CB CYS D1127 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1127 " pdb=" CB CYS B1127 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 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 93.00 152.91 -59.91 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 25559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 6479 0.308 - 0.617: 31 0.617 - 0.925: 0 0.925 - 1.234: 0 1.234 - 1.542: 4 Chirality restraints: 6514 Sorted by residual: 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 -2.76 0.36 2.00e-02 2.50e+03 3.16e+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 2.42e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 6511 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.175 2.00e-02 2.50e+03 1.48e-01 2.74e+02 pdb=" C7 NAG L 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.238 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.162 2.00e-02 2.50e+03 1.37e-01 2.34e+02 pdb=" C7 NAG H 1 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.163 2.00e-02 2.50e+03 1.35e-01 2.28e+02 pdb=" C7 NAG E 2 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.218 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 245 2.39 - 3.02: 26835 3.02 - 3.65: 62657 3.65 - 4.27: 89987 4.27 - 4.90: 143593 Nonbonded interactions: 323317 Sorted by model distance: nonbonded pdb=" O GLY C 952 " pdb=" NH1 ARG C1297 " model vdw 1.769 3.120 nonbonded pdb=" SD MET C 959 " pdb=" NE2 GLN C 995 " model vdw 1.802 3.480 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.867 3.040 nonbonded pdb=" SD MET A 959 " pdb=" NE2 GLN A 995 " model vdw 1.874 3.480 nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.878 3.040 ... (remaining 323312 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 1337 or resid 2001 through 2005)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 1337 or resid 2001 through 2005)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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: 2.490 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: 0.050 Extract box with map and model: 0.470 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 31.790 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.010 0.297 41504 Z= 0.493 Angle : 1.560 25.882 56478 Z= 0.895 Chirality : 0.081 1.542 6514 Planarity : 0.009 0.148 7202 Dihedral : 15.204 107.530 15830 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 1.45 % Allowed : 14.50 % Favored : 84.05 % Rotamer: Outliers : 0.63 % Allowed : 4.85 % Favored : 94.52 % Cbeta Deviations : 0.21 % 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: -4.14 (0.10), residues: 5110 helix: -0.89 (0.15), residues: 856 sheet: -2.05 (0.10), residues: 1858 loop : -4.12 (0.10), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 360 TYR 0.041 0.003 TYR C 166 PHE 0.030 0.003 PHE B 155 TRP 0.016 0.003 TRP D 765 HIS 0.015 0.002 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00975 (41420) covalent geometry : angle 1.53776 (56270) SS BOND : bond 0.00378 ( 44) SS BOND : angle 2.88312 ( 88) hydrogen bonds : bond 0.09102 ( 540) hydrogen bonds : angle 6.32581 ( 1620) link_BETA1-4 : bond 0.03275 ( 12) link_BETA1-4 : angle 7.90904 ( 36) link_NAG-ASN : bond 0.01645 ( 28) link_NAG-ASN : angle 4.11030 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 851 time to evaluate : 1.607 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: A 50 LEU cc_start: 0.8151 (tt) cc_final: 0.7838 (tt) REVERT: A 203 TYR cc_start: 0.6196 (m-10) cc_final: 0.5830 (m-80) REVERT: A 208 GLN cc_start: 0.7860 (tt0) cc_final: 0.7534 (tp40) REVERT: A 384 ILE cc_start: 0.9459 (pt) cc_final: 0.9127 (mm) REVERT: A 456 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8602 (mmmt) REVERT: A 458 PHE cc_start: 0.7986 (p90) cc_final: 0.7756 (p90) REVERT: A 567 LYS cc_start: 0.8319 (tppt) cc_final: 0.8072 (tppt) REVERT: A 672 ASP cc_start: 0.8422 (t0) cc_final: 0.8200 (t0) REVERT: A 766 LYS cc_start: 0.6957 (mmtp) cc_final: 0.6713 (mptt) REVERT: A 828 LEU cc_start: 0.7951 (pt) cc_final: 0.6938 (pp) REVERT: A 931 LEU cc_start: 0.9160 (tp) cc_final: 0.8949 (tp) REVERT: A 988 ASP cc_start: 0.9012 (m-30) cc_final: 0.8329 (m-30) REVERT: A 1015 GLN cc_start: 0.8202 (tp40) cc_final: 0.7742 (tp40) REVERT: A 1035 ASN cc_start: 0.6454 (m110) cc_final: 0.6095 (m110) REVERT: A 1161 ASP cc_start: 0.9030 (p0) cc_final: 0.8784 (p0) REVERT: A 1165 GLU cc_start: 0.9133 (tt0) cc_final: 0.8843 (tt0) REVERT: A 1217 LEU cc_start: 0.9586 (mm) cc_final: 0.9339 (mm) REVERT: A 1314 MET cc_start: 0.8748 (mpp) cc_final: 0.8284 (mpp) REVERT: A 1323 TYR cc_start: 0.7304 (t80) cc_final: 0.6954 (t80) REVERT: B 134 ASP cc_start: 0.8351 (t0) cc_final: 0.7543 (t70) REVERT: B 183 LEU cc_start: 0.7730 (mt) cc_final: 0.7479 (mt) REVERT: B 208 GLN cc_start: 0.7935 (tt0) cc_final: 0.7698 (tp-100) REVERT: B 532 SER cc_start: 0.7150 (t) cc_final: 0.6944 (m) REVERT: B 561 GLU cc_start: 0.7418 (pt0) cc_final: 0.6839 (pt0) REVERT: B 605 LEU cc_start: 0.8613 (tp) cc_final: 0.8305 (tp) REVERT: B 688 MET cc_start: 0.8262 (ppp) cc_final: 0.7905 (ppp) REVERT: B 741 TRP cc_start: 0.8007 (t-100) cc_final: 0.7388 (t-100) REVERT: B 787 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7380 (mtm180) REVERT: B 858 TRP cc_start: 0.7775 (m-90) cc_final: 0.7296 (m-90) REVERT: B 1105 ILE cc_start: 0.8878 (mt) cc_final: 0.8653 (mt) REVERT: B 1147 LYS cc_start: 0.8985 (mttp) cc_final: 0.8553 (mttp) REVERT: B 1149 LEU cc_start: 0.9611 (tp) cc_final: 0.9408 (tt) REVERT: B 1161 ASP cc_start: 0.8914 (p0) cc_final: 0.8521 (p0) REVERT: B 1172 GLU cc_start: 0.9031 (tt0) cc_final: 0.8318 (tm-30) REVERT: B 1229 THR cc_start: 0.9058 (p) cc_final: 0.8843 (p) REVERT: B 1241 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8532 (tm-30) REVERT: B 1330 TYR cc_start: 0.8312 (p90) cc_final: 0.8081 (p90) REVERT: C 50 LEU cc_start: 0.8134 (tt) cc_final: 0.7805 (tt) REVERT: C 203 TYR cc_start: 0.6209 (m-10) cc_final: 0.5843 (m-80) REVERT: C 208 GLN cc_start: 0.7781 (tt0) cc_final: 0.7456 (tp40) REVERT: C 260 VAL cc_start: 0.4773 (p) cc_final: 0.4528 (p) REVERT: C 384 ILE cc_start: 0.9458 (pt) cc_final: 0.9135 (mm) REVERT: C 456 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8593 (mmmt) REVERT: C 458 PHE cc_start: 0.7960 (p90) cc_final: 0.7752 (p90) REVERT: C 567 LYS cc_start: 0.8336 (tppt) cc_final: 0.8089 (tppt) REVERT: C 672 ASP cc_start: 0.8415 (t0) cc_final: 0.8202 (t0) REVERT: C 828 LEU cc_start: 0.7962 (pt) cc_final: 0.6926 (pp) REVERT: C 931 LEU cc_start: 0.9158 (tp) cc_final: 0.8946 (tp) REVERT: C 977 MET cc_start: 0.9145 (mmm) cc_final: 0.8887 (mmm) REVERT: C 988 ASP cc_start: 0.8988 (m-30) cc_final: 0.8301 (m-30) REVERT: C 1015 GLN cc_start: 0.8201 (tp40) cc_final: 0.7571 (tp40) REVERT: C 1035 ASN cc_start: 0.6623 (m110) cc_final: 0.6163 (m110) REVERT: C 1161 ASP cc_start: 0.8997 (p0) cc_final: 0.8735 (p0) REVERT: C 1165 GLU cc_start: 0.9148 (tt0) cc_final: 0.8848 (tt0) REVERT: C 1217 LEU cc_start: 0.9576 (mm) cc_final: 0.9328 (mm) REVERT: C 1314 MET cc_start: 0.8858 (mpp) cc_final: 0.8403 (mpp) REVERT: C 1323 TYR cc_start: 0.7190 (t80) cc_final: 0.6788 (t80) REVERT: D 134 ASP cc_start: 0.8285 (t0) cc_final: 0.7524 (t70) REVERT: D 183 LEU cc_start: 0.7778 (mt) cc_final: 0.7497 (mt) REVERT: D 561 GLU cc_start: 0.7324 (pt0) cc_final: 0.6744 (pt0) REVERT: D 605 LEU cc_start: 0.8679 (tp) cc_final: 0.8374 (tp) REVERT: D 673 MET cc_start: 0.8245 (tpp) cc_final: 0.7974 (tpp) REVERT: D 688 MET cc_start: 0.8328 (ppp) cc_final: 0.7952 (ppp) REVERT: D 741 TRP cc_start: 0.8021 (t-100) cc_final: 0.7379 (t-100) REVERT: D 787 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7299 (mtm180) REVERT: D 858 TRP cc_start: 0.7641 (m-90) cc_final: 0.7209 (m-90) REVERT: D 1105 ILE cc_start: 0.8833 (mt) cc_final: 0.8605 (mt) REVERT: D 1161 ASP cc_start: 0.8897 (p0) cc_final: 0.8482 (p0) REVERT: D 1229 THR cc_start: 0.9050 (p) cc_final: 0.8839 (p) REVERT: D 1241 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8533 (tm-30) outliers start: 28 outliers final: 20 residues processed: 869 average time/residue: 0.2281 time to fit residues: 331.3690 Evaluate side-chains 593 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 573 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 960 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 960 GLN Chi-restraints excluded: chain D residue 965 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 217 HIS A 851 ASN A 854 GLN A 960 GLN A 963 GLN A 983 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN B 30 GLN B 132 GLN B 177 GLN B 413 ASN B 424 ASN B 479 HIS B 511 HIS B 693 GLN B 960 GLN B 976 ASN B1020 HIS B1035 ASN B1038 ASN B1089 ASN C 124 ASN C 132 GLN C 217 HIS C 851 ASN C 854 GLN C 960 GLN C 963 GLN C 983 ASN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 132 GLN D 177 GLN D 413 ASN D 424 ASN D 479 HIS D 511 HIS D 693 GLN D 960 GLN D 983 ASN D1020 HIS D1038 ASN D1089 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.110859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.089158 restraints weight = 118428.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.092521 restraints weight = 63242.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094852 restraints weight = 40513.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.096474 restraints weight = 29138.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.097632 restraints weight = 22933.877| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 41504 Z= 0.185 Angle : 0.913 14.098 56478 Z= 0.446 Chirality : 0.052 0.516 6514 Planarity : 0.006 0.067 7202 Dihedral : 9.014 70.653 6348 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.47 % Favored : 90.25 % Rotamer: Outliers : 2.68 % Allowed : 14.09 % Favored : 83.22 % 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: -3.14 (0.11), residues: 5110 helix: 0.36 (0.17), residues: 848 sheet: -1.65 (0.11), residues: 1860 loop : -3.42 (0.11), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 370 TYR 0.041 0.002 TYR C 649 PHE 0.022 0.002 PHE D 74 TRP 0.026 0.002 TRP B1237 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00411 (41420) covalent geometry : angle 0.89573 (56270) SS BOND : bond 0.00262 ( 44) SS BOND : angle 2.01269 ( 88) hydrogen bonds : bond 0.05852 ( 540) hydrogen bonds : angle 5.28295 ( 1620) link_BETA1-4 : bond 0.00660 ( 12) link_BETA1-4 : angle 3.29521 ( 36) link_NAG-ASN : bond 0.01260 ( 28) link_NAG-ASN : angle 3.79659 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 694 time to evaluate : 1.586 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: A 101 MET cc_start: 0.8392 (mtp) cc_final: 0.7561 (mmm) REVERT: A 114 PHE cc_start: 0.6854 (t80) cc_final: 0.6652 (t80) REVERT: A 192 PHE cc_start: 0.7872 (t80) cc_final: 0.7653 (t80) REVERT: A 208 GLN cc_start: 0.7706 (tt0) cc_final: 0.7502 (tp-100) REVERT: A 384 ILE cc_start: 0.9465 (pt) cc_final: 0.9156 (mm) REVERT: A 387 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7964 (mtt-85) REVERT: A 415 MET cc_start: 0.6328 (ppp) cc_final: 0.5913 (ppp) REVERT: A 456 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8740 (mmmt) REVERT: A 458 PHE cc_start: 0.8160 (p90) cc_final: 0.7938 (p90) REVERT: A 672 ASP cc_start: 0.8540 (t0) cc_final: 0.8249 (t0) REVERT: A 787 ARG cc_start: 0.8459 (ptt-90) cc_final: 0.8160 (ptt-90) REVERT: A 934 LYS cc_start: 0.8350 (tppt) cc_final: 0.8088 (mmmt) REVERT: A 965 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 988 ASP cc_start: 0.8956 (m-30) cc_final: 0.8579 (m-30) REVERT: A 1161 ASP cc_start: 0.8950 (p0) cc_final: 0.8646 (p0) REVERT: A 1165 GLU cc_start: 0.9119 (tt0) cc_final: 0.8845 (tt0) REVERT: A 1217 LEU cc_start: 0.9617 (mm) cc_final: 0.9286 (mp) REVERT: A 1314 MET cc_start: 0.8761 (mpp) cc_final: 0.8310 (mpp) REVERT: A 1323 TYR cc_start: 0.7239 (t80) cc_final: 0.6987 (t80) REVERT: B 134 ASP cc_start: 0.8113 (t0) cc_final: 0.7577 (t70) REVERT: B 183 LEU cc_start: 0.7971 (mt) cc_final: 0.7758 (mt) REVERT: B 208 GLN cc_start: 0.7928 (tt0) cc_final: 0.7679 (tp-100) REVERT: B 222 GLU cc_start: 0.8412 (pt0) cc_final: 0.8098 (pp20) REVERT: B 318 MET cc_start: 0.5344 (mmm) cc_final: 0.5109 (mmm) REVERT: B 372 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 387 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7468 (ttm-80) REVERT: B 500 MET cc_start: 0.6975 (ttt) cc_final: 0.6736 (ttt) REVERT: B 519 ASP cc_start: 0.6538 (m-30) cc_final: 0.6253 (m-30) REVERT: B 561 GLU cc_start: 0.7294 (pt0) cc_final: 0.6816 (pt0) REVERT: B 605 LEU cc_start: 0.8444 (tp) cc_final: 0.8061 (tp) REVERT: B 627 LEU cc_start: 0.9134 (tp) cc_final: 0.8906 (tt) REVERT: B 673 MET cc_start: 0.8596 (tpp) cc_final: 0.8281 (tpp) REVERT: B 741 TRP cc_start: 0.8127 (t-100) cc_final: 0.7468 (t-100) REVERT: B 858 TRP cc_start: 0.7577 (m-90) cc_final: 0.7021 (m-90) REVERT: B 965 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7556 (mm) REVERT: B 977 MET cc_start: 0.9220 (mmm) cc_final: 0.8815 (mmm) REVERT: B 992 GLU cc_start: 0.8151 (tp30) cc_final: 0.7738 (tp30) REVERT: B 1161 ASP cc_start: 0.8811 (p0) cc_final: 0.8372 (p0) REVERT: B 1168 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8694 (tttm) REVERT: B 1172 GLU cc_start: 0.9001 (tt0) cc_final: 0.8285 (tm-30) REVERT: B 1323 TYR cc_start: 0.7379 (t80) cc_final: 0.7130 (t80) REVERT: C 31 TYR cc_start: 0.7208 (p90) cc_final: 0.6978 (p90) REVERT: C 114 PHE cc_start: 0.6862 (t80) cc_final: 0.6639 (t80) REVERT: C 121 MET cc_start: 0.7451 (ttt) cc_final: 0.7187 (ttt) REVERT: C 192 PHE cc_start: 0.7888 (t80) cc_final: 0.7662 (t80) REVERT: C 384 ILE cc_start: 0.9469 (pt) cc_final: 0.9116 (mm) REVERT: C 415 MET cc_start: 0.6361 (ppp) cc_final: 0.5919 (ppp) REVERT: C 456 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8740 (mmmt) REVERT: C 458 PHE cc_start: 0.8231 (p90) cc_final: 0.8029 (p90) REVERT: C 672 ASP cc_start: 0.8540 (t0) cc_final: 0.8249 (t0) REVERT: C 787 ARG cc_start: 0.8445 (ptt-90) cc_final: 0.8138 (ptt-90) REVERT: C 934 LYS cc_start: 0.8321 (tppt) cc_final: 0.8083 (mmmt) REVERT: C 965 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8346 (mm) REVERT: C 977 MET cc_start: 0.9270 (mmm) cc_final: 0.9047 (mmm) REVERT: C 988 ASP cc_start: 0.8972 (m-30) cc_final: 0.8640 (m-30) REVERT: C 1015 GLN cc_start: 0.8396 (tp40) cc_final: 0.7895 (tp40) REVERT: C 1161 ASP cc_start: 0.8940 (p0) cc_final: 0.8626 (p0) REVERT: C 1165 GLU cc_start: 0.9140 (tt0) cc_final: 0.8849 (tt0) REVERT: C 1217 LEU cc_start: 0.9612 (mm) cc_final: 0.9269 (mp) REVERT: C 1314 MET cc_start: 0.8764 (mpp) cc_final: 0.8315 (mpp) REVERT: C 1323 TYR cc_start: 0.7188 (t80) cc_final: 0.6879 (t80) REVERT: D 67 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (p) REVERT: D 134 ASP cc_start: 0.8109 (t0) cc_final: 0.7607 (t70) REVERT: D 183 LEU cc_start: 0.7937 (mt) cc_final: 0.7734 (mt) REVERT: D 222 GLU cc_start: 0.8416 (pt0) cc_final: 0.8090 (pp20) REVERT: D 318 MET cc_start: 0.5402 (mmm) cc_final: 0.5127 (mmm) REVERT: D 372 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8302 (p) REVERT: D 387 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7722 (ttm-80) REVERT: D 500 MET cc_start: 0.7001 (ttt) cc_final: 0.6583 (ttt) REVERT: D 561 GLU cc_start: 0.7240 (pt0) cc_final: 0.6759 (pt0) REVERT: D 605 LEU cc_start: 0.8444 (tp) cc_final: 0.8073 (tp) REVERT: D 627 LEU cc_start: 0.9181 (tp) cc_final: 0.8980 (tt) REVERT: D 673 MET cc_start: 0.8628 (tpp) cc_final: 0.8234 (tpp) REVERT: D 741 TRP cc_start: 0.8141 (t-100) cc_final: 0.7448 (t-100) REVERT: D 858 TRP cc_start: 0.7596 (m-90) cc_final: 0.7025 (m-90) REVERT: D 977 MET cc_start: 0.9198 (mmm) cc_final: 0.8831 (mmm) REVERT: D 990 LEU cc_start: 0.8478 (mt) cc_final: 0.8233 (mp) REVERT: D 992 GLU cc_start: 0.8238 (tp30) cc_final: 0.7769 (tp30) REVERT: D 1018 TYR cc_start: 0.7940 (m-80) cc_final: 0.7560 (m-80) REVERT: D 1149 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9286 (tt) REVERT: D 1161 ASP cc_start: 0.8824 (p0) cc_final: 0.8400 (p0) REVERT: D 1168 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8726 (tttm) REVERT: D 1323 TYR cc_start: 0.7380 (t80) cc_final: 0.7149 (t80) outliers start: 120 outliers final: 66 residues processed: 762 average time/residue: 0.2109 time to fit residues: 276.6395 Evaluate side-chains 649 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 576 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1125 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1315 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 646 HIS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1125 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1315 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 311 optimal weight: 0.0470 chunk 306 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 502 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 418 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN A 691 GLN A 851 ASN A1020 HIS ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 310 GLN B 961 ASN C 644 ASN C 646 HIS C 691 GLN C 851 ASN C1020 HIS C1179 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 310 GLN D 691 GLN D 961 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.108502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.086496 restraints weight = 118246.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.089746 restraints weight = 63179.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092051 restraints weight = 40833.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.093643 restraints weight = 29496.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094726 restraints weight = 23338.650| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41504 Z= 0.175 Angle : 0.864 36.326 56478 Z= 0.415 Chirality : 0.050 0.372 6514 Planarity : 0.005 0.072 7202 Dihedral : 7.628 58.355 6309 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.98 % Favored : 89.78 % Rotamer: Outliers : 3.74 % Allowed : 16.62 % Favored : 79.64 % 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: -2.64 (0.11), residues: 5110 helix: 0.74 (0.17), residues: 854 sheet: -1.27 (0.11), residues: 1834 loop : -3.16 (0.11), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 645 TYR 0.029 0.002 TYR D1007 PHE 0.035 0.002 PHE D 114 TRP 0.028 0.002 TRP A 741 HIS 0.009 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00380 (41420) covalent geometry : angle 0.82197 (56270) SS BOND : bond 0.00917 ( 44) SS BOND : angle 2.44047 ( 88) hydrogen bonds : bond 0.05236 ( 540) hydrogen bonds : angle 5.28224 ( 1620) link_BETA1-4 : bond 0.00457 ( 12) link_BETA1-4 : angle 3.00777 ( 36) link_NAG-ASN : bond 0.00839 ( 28) link_NAG-ASN : angle 6.27535 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 654 time to evaluate : 1.468 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: A 66 SER cc_start: 0.8562 (t) cc_final: 0.7707 (p) REVERT: A 138 TYR cc_start: 0.7928 (m-80) cc_final: 0.7633 (m-80) REVERT: A 169 ASP cc_start: 0.6415 (m-30) cc_final: 0.5206 (m-30) REVERT: A 173 ASN cc_start: 0.6154 (m-40) cc_final: 0.5679 (p0) REVERT: A 384 ILE cc_start: 0.9525 (pt) cc_final: 0.9132 (mm) REVERT: A 456 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8755 (mmmt) REVERT: A 458 PHE cc_start: 0.8289 (p90) cc_final: 0.8087 (p90) REVERT: A 567 LYS cc_start: 0.8342 (tppt) cc_final: 0.8035 (tppt) REVERT: A 656 THR cc_start: -0.1893 (OUTLIER) cc_final: -0.2389 (p) REVERT: A 672 ASP cc_start: 0.8603 (t0) cc_final: 0.8333 (t0) REVERT: A 778 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6952 (pt) REVERT: A 965 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 988 ASP cc_start: 0.8993 (m-30) cc_final: 0.8638 (m-30) REVERT: A 1018 TYR cc_start: 0.8280 (m-80) cc_final: 0.8034 (m-80) REVERT: A 1109 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9005 (mm) REVERT: A 1161 ASP cc_start: 0.8948 (p0) cc_final: 0.8638 (p0) REVERT: A 1165 GLU cc_start: 0.9154 (tt0) cc_final: 0.8867 (tt0) REVERT: A 1217 LEU cc_start: 0.9620 (mm) cc_final: 0.9368 (mm) REVERT: A 1314 MET cc_start: 0.8768 (mpp) cc_final: 0.8273 (mpp) REVERT: B 134 ASP cc_start: 0.8243 (t0) cc_final: 0.7702 (t70) REVERT: B 183 LEU cc_start: 0.7870 (mt) cc_final: 0.7653 (mt) REVERT: B 208 GLN cc_start: 0.7947 (tt0) cc_final: 0.7675 (tp-100) REVERT: B 222 GLU cc_start: 0.8416 (pt0) cc_final: 0.8084 (pp20) REVERT: B 318 MET cc_start: 0.5605 (mmm) cc_final: 0.5075 (tpt) REVERT: B 373 ASP cc_start: 0.8392 (p0) cc_final: 0.8001 (t0) REVERT: B 500 MET cc_start: 0.7009 (ttt) cc_final: 0.6718 (ttt) REVERT: B 543 TYR cc_start: 0.7897 (p90) cc_final: 0.7612 (p90) REVERT: B 561 GLU cc_start: 0.7353 (pt0) cc_final: 0.6905 (pt0) REVERT: B 578 LEU cc_start: 0.8398 (mt) cc_final: 0.8046 (pt) REVERT: B 605 LEU cc_start: 0.8503 (tp) cc_final: 0.8098 (tp) REVERT: B 627 LEU cc_start: 0.9148 (tp) cc_final: 0.8927 (tt) REVERT: B 656 THR cc_start: -0.2208 (OUTLIER) cc_final: -0.2752 (t) REVERT: B 669 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8492 (t80) REVERT: B 673 MET cc_start: 0.8539 (tpp) cc_final: 0.8123 (tpp) REVERT: B 741 TRP cc_start: 0.8240 (t-100) cc_final: 0.7470 (t-100) REVERT: B 782 SER cc_start: 0.8043 (t) cc_final: 0.7683 (m) REVERT: B 858 TRP cc_start: 0.7533 (m-90) cc_final: 0.6959 (m-90) REVERT: B 965 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7562 (mm) REVERT: B 977 MET cc_start: 0.9245 (mmm) cc_final: 0.8745 (mmm) REVERT: B 1018 TYR cc_start: 0.8072 (m-80) cc_final: 0.7633 (m-80) REVERT: B 1161 ASP cc_start: 0.8904 (p0) cc_final: 0.8493 (p0) REVERT: B 1168 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8781 (ptmm) REVERT: B 1172 GLU cc_start: 0.9002 (tt0) cc_final: 0.8212 (tm-30) REVERT: B 1217 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9128 (mm) REVERT: B 1258 LEU cc_start: 0.8906 (mt) cc_final: 0.8541 (mp) REVERT: C 66 SER cc_start: 0.8520 (t) cc_final: 0.7628 (p) REVERT: C 169 ASP cc_start: 0.6412 (m-30) cc_final: 0.5196 (m-30) REVERT: C 173 ASN cc_start: 0.6123 (m-40) cc_final: 0.5650 (p0) REVERT: C 384 ILE cc_start: 0.9542 (pt) cc_final: 0.9138 (mm) REVERT: C 456 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8751 (mmmt) REVERT: C 567 LYS cc_start: 0.8357 (tppt) cc_final: 0.8047 (tppt) REVERT: C 656 THR cc_start: -0.2131 (OUTLIER) cc_final: -0.2648 (p) REVERT: C 672 ASP cc_start: 0.8581 (t0) cc_final: 0.8297 (t0) REVERT: C 778 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6987 (pt) REVERT: C 965 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8323 (mm) REVERT: C 977 MET cc_start: 0.9295 (mmm) cc_final: 0.9019 (mmm) REVERT: C 988 ASP cc_start: 0.9003 (m-30) cc_final: 0.8642 (m-30) REVERT: C 1015 GLN cc_start: 0.8351 (tp40) cc_final: 0.7766 (tp40) REVERT: C 1109 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9026 (mm) REVERT: C 1161 ASP cc_start: 0.8930 (p0) cc_final: 0.8611 (p0) REVERT: C 1165 GLU cc_start: 0.9165 (tt0) cc_final: 0.8863 (tt0) REVERT: C 1217 LEU cc_start: 0.9628 (mm) cc_final: 0.9409 (mm) REVERT: C 1314 MET cc_start: 0.8819 (mpp) cc_final: 0.8289 (mpp) REVERT: C 1323 TYR cc_start: 0.7369 (t80) cc_final: 0.7092 (t80) REVERT: D 134 ASP cc_start: 0.8209 (t0) cc_final: 0.7726 (t70) REVERT: D 183 LEU cc_start: 0.7937 (mt) cc_final: 0.7695 (mt) REVERT: D 222 GLU cc_start: 0.8412 (pt0) cc_final: 0.8089 (pp20) REVERT: D 318 MET cc_start: 0.5660 (mmm) cc_final: 0.5209 (tpt) REVERT: D 373 ASP cc_start: 0.8383 (p0) cc_final: 0.8112 (t0) REVERT: D 500 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6445 (ttm) REVERT: D 541 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6377 (pt) REVERT: D 561 GLU cc_start: 0.7312 (pt0) cc_final: 0.6805 (pt0) REVERT: D 578 LEU cc_start: 0.8409 (mt) cc_final: 0.8055 (pt) REVERT: D 605 LEU cc_start: 0.8500 (tp) cc_final: 0.8100 (tp) REVERT: D 656 THR cc_start: -0.1956 (OUTLIER) cc_final: -0.2477 (t) REVERT: D 673 MET cc_start: 0.8546 (tpp) cc_final: 0.8099 (tpp) REVERT: D 741 TRP cc_start: 0.8256 (t-100) cc_final: 0.7507 (t-100) REVERT: D 782 SER cc_start: 0.8011 (t) cc_final: 0.7660 (m) REVERT: D 858 TRP cc_start: 0.7542 (m-90) cc_final: 0.6988 (m-90) REVERT: D 863 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8735 (mtpt) REVERT: D 977 MET cc_start: 0.9299 (mmm) cc_final: 0.8866 (mmm) REVERT: D 990 LEU cc_start: 0.8588 (mt) cc_final: 0.8369 (mp) REVERT: D 1018 TYR cc_start: 0.8020 (m-80) cc_final: 0.7610 (m-80) REVERT: D 1147 LYS cc_start: 0.8899 (mttp) cc_final: 0.8440 (mttp) REVERT: D 1149 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9319 (tt) REVERT: D 1161 ASP cc_start: 0.8923 (p0) cc_final: 0.8531 (p0) REVERT: D 1168 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8768 (ptmm) REVERT: D 1217 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9131 (mm) REVERT: D 1258 LEU cc_start: 0.8908 (mt) cc_final: 0.8544 (mp) outliers start: 167 outliers final: 63 residues processed: 765 average time/residue: 0.2039 time to fit residues: 270.9012 Evaluate side-chains 665 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 585 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 646 HIS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 341 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 371 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 406 optimal weight: 0.0570 chunk 392 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 381 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 385 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A1242 GLN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN B 85 HIS B1242 GLN ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN C 983 ASN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 961 ASN D 983 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.109636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.087651 restraints weight = 116912.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090903 restraints weight = 62590.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.093230 restraints weight = 40535.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094849 restraints weight = 29248.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.095959 restraints weight = 23084.634| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41504 Z= 0.139 Angle : 0.816 26.575 56478 Z= 0.387 Chirality : 0.049 0.352 6514 Planarity : 0.005 0.069 7202 Dihedral : 7.216 58.604 6302 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.77 % Favored : 91.00 % Rotamer: Outliers : 3.62 % Allowed : 18.43 % Favored : 77.94 % 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: -2.33 (0.11), residues: 5110 helix: 1.01 (0.18), residues: 850 sheet: -1.04 (0.12), residues: 1826 loop : -2.98 (0.11), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 370 TYR 0.027 0.002 TYR D1007 PHE 0.040 0.002 PHE D 808 TRP 0.020 0.001 TRP B1237 HIS 0.020 0.001 HIS C 646 Details of bonding type rmsd covalent geometry : bond 0.00308 (41420) covalent geometry : angle 0.78535 (56270) SS BOND : bond 0.00863 ( 44) SS BOND : angle 2.04577 ( 88) hydrogen bonds : bond 0.04906 ( 540) hydrogen bonds : angle 5.06646 ( 1620) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 2.82441 ( 36) link_NAG-ASN : bond 0.00788 ( 28) link_NAG-ASN : angle 5.14423 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 630 time to evaluate : 1.489 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: A 66 SER cc_start: 0.8620 (t) cc_final: 0.7830 (p) REVERT: A 169 ASP cc_start: 0.6473 (m-30) cc_final: 0.6198 (m-30) REVERT: A 309 PHE cc_start: 0.8628 (m-80) cc_final: 0.7928 (m-80) REVERT: A 310 GLN cc_start: 0.8500 (mp-120) cc_final: 0.8241 (mp10) REVERT: A 384 ILE cc_start: 0.9555 (pt) cc_final: 0.9135 (mm) REVERT: A 456 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8668 (mmmt) REVERT: A 656 THR cc_start: -0.2189 (OUTLIER) cc_final: -0.2585 (p) REVERT: A 672 ASP cc_start: 0.8587 (t0) cc_final: 0.8291 (t0) REVERT: A 778 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6971 (pt) REVERT: A 965 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8221 (mm) REVERT: A 977 MET cc_start: 0.9244 (mmm) cc_final: 0.8794 (mmm) REVERT: A 988 ASP cc_start: 0.8984 (m-30) cc_final: 0.8591 (m-30) REVERT: A 1015 GLN cc_start: 0.7996 (tp40) cc_final: 0.7793 (tp40) REVERT: A 1018 TYR cc_start: 0.8327 (m-80) cc_final: 0.8122 (m-80) REVERT: A 1109 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8985 (mm) REVERT: A 1149 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9336 (tt) REVERT: A 1161 ASP cc_start: 0.8951 (p0) cc_final: 0.8618 (p0) REVERT: A 1165 GLU cc_start: 0.9175 (tt0) cc_final: 0.8884 (tt0) REVERT: A 1217 LEU cc_start: 0.9620 (mm) cc_final: 0.9389 (mm) REVERT: A 1242 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7946 (tp40) REVERT: A 1298 LEU cc_start: 0.8617 (tp) cc_final: 0.8386 (mp) REVERT: A 1305 LEU cc_start: 0.8207 (mt) cc_final: 0.8001 (mp) REVERT: A 1314 MET cc_start: 0.8795 (mpp) cc_final: 0.8258 (mpp) REVERT: B 74 PHE cc_start: 0.8476 (t80) cc_final: 0.8110 (t80) REVERT: B 134 ASP cc_start: 0.8239 (t0) cc_final: 0.7717 (t70) REVERT: B 208 GLN cc_start: 0.7937 (tt0) cc_final: 0.7630 (tp-100) REVERT: B 222 GLU cc_start: 0.8451 (pt0) cc_final: 0.8078 (pp20) REVERT: B 246 MET cc_start: 0.7763 (mtm) cc_final: 0.7551 (mtp) REVERT: B 318 MET cc_start: 0.5610 (mmm) cc_final: 0.5021 (tpt) REVERT: B 373 ASP cc_start: 0.8274 (p0) cc_final: 0.7868 (t0) REVERT: B 561 GLU cc_start: 0.7246 (pt0) cc_final: 0.6738 (pt0) REVERT: B 578 LEU cc_start: 0.8298 (mt) cc_final: 0.7895 (pp) REVERT: B 605 LEU cc_start: 0.8497 (tp) cc_final: 0.8094 (tp) REVERT: B 673 MET cc_start: 0.8552 (tpp) cc_final: 0.8062 (tpp) REVERT: B 688 MET cc_start: 0.8286 (ppp) cc_final: 0.8000 (ppp) REVERT: B 741 TRP cc_start: 0.8162 (t-100) cc_final: 0.7446 (t-100) REVERT: B 782 SER cc_start: 0.8023 (t) cc_final: 0.7758 (m) REVERT: B 786 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7105 (tt) REVERT: B 798 MET cc_start: 0.8673 (ptm) cc_final: 0.8439 (ptt) REVERT: B 858 TRP cc_start: 0.7557 (m-90) cc_final: 0.7016 (m-90) REVERT: B 965 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7702 (mm) REVERT: B 977 MET cc_start: 0.9226 (mmm) cc_final: 0.8735 (mmm) REVERT: B 1018 TYR cc_start: 0.7994 (m-80) cc_final: 0.7651 (m-10) REVERT: B 1161 ASP cc_start: 0.8898 (p0) cc_final: 0.8480 (p0) REVERT: B 1168 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8753 (pttp) REVERT: B 1172 GLU cc_start: 0.8991 (tt0) cc_final: 0.8214 (tm-30) REVERT: B 1217 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9103 (mm) REVERT: C 66 SER cc_start: 0.8618 (t) cc_final: 0.7819 (p) REVERT: C 169 ASP cc_start: 0.6489 (m-30) cc_final: 0.6204 (m-30) REVERT: C 245 GLU cc_start: 0.8728 (pp20) cc_final: 0.8204 (pp20) REVERT: C 309 PHE cc_start: 0.8637 (m-80) cc_final: 0.7944 (m-80) REVERT: C 310 GLN cc_start: 0.8473 (mp-120) cc_final: 0.8220 (mp10) REVERT: C 384 ILE cc_start: 0.9564 (pt) cc_final: 0.9118 (mm) REVERT: C 456 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8671 (mmmt) REVERT: C 656 THR cc_start: -0.2075 (OUTLIER) cc_final: -0.2457 (p) REVERT: C 672 ASP cc_start: 0.8578 (t0) cc_final: 0.8274 (t0) REVERT: C 778 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7028 (pt) REVERT: C 965 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8282 (mm) REVERT: C 977 MET cc_start: 0.9302 (mmm) cc_final: 0.9018 (mmm) REVERT: C 988 ASP cc_start: 0.8957 (m-30) cc_final: 0.8584 (m-30) REVERT: C 1015 GLN cc_start: 0.8321 (tp40) cc_final: 0.7870 (tp40) REVERT: C 1109 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8999 (mm) REVERT: C 1149 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9346 (tt) REVERT: C 1161 ASP cc_start: 0.8949 (p0) cc_final: 0.8614 (p0) REVERT: C 1165 GLU cc_start: 0.9182 (tt0) cc_final: 0.8877 (tt0) REVERT: C 1217 LEU cc_start: 0.9628 (mm) cc_final: 0.9388 (mm) REVERT: C 1314 MET cc_start: 0.8832 (mpp) cc_final: 0.8294 (mpp) REVERT: D 74 PHE cc_start: 0.8439 (t80) cc_final: 0.8102 (t80) REVERT: D 134 ASP cc_start: 0.8236 (t0) cc_final: 0.7506 (t70) REVERT: D 222 GLU cc_start: 0.8460 (pt0) cc_final: 0.8071 (pp20) REVERT: D 246 MET cc_start: 0.7646 (mtm) cc_final: 0.7403 (mtp) REVERT: D 318 MET cc_start: 0.5634 (mmm) cc_final: 0.5106 (tpt) REVERT: D 372 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.7993 (p) REVERT: D 387 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7515 (ttm-80) REVERT: D 500 MET cc_start: 0.6592 (ttt) cc_final: 0.6355 (ttt) REVERT: D 541 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6166 (pt) REVERT: D 561 GLU cc_start: 0.7202 (pt0) cc_final: 0.6663 (pt0) REVERT: D 578 LEU cc_start: 0.8314 (mt) cc_final: 0.7906 (pp) REVERT: D 605 LEU cc_start: 0.8544 (tp) cc_final: 0.8149 (tp) REVERT: D 669 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (t80) REVERT: D 673 MET cc_start: 0.8556 (tpp) cc_final: 0.8108 (tpp) REVERT: D 741 TRP cc_start: 0.8179 (t-100) cc_final: 0.7384 (t-100) REVERT: D 782 SER cc_start: 0.7982 (t) cc_final: 0.7725 (m) REVERT: D 786 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7099 (tt) REVERT: D 858 TRP cc_start: 0.7511 (m-90) cc_final: 0.7027 (m-90) REVERT: D 977 MET cc_start: 0.9297 (mmm) cc_final: 0.8731 (mmm) REVERT: D 1018 TYR cc_start: 0.7992 (m-80) cc_final: 0.7654 (m-10) REVERT: D 1035 ASN cc_start: 0.7901 (m-40) cc_final: 0.7646 (m-40) REVERT: D 1149 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9298 (tt) REVERT: D 1161 ASP cc_start: 0.8924 (p0) cc_final: 0.8519 (p0) REVERT: D 1168 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8766 (pttp) REVERT: D 1217 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9108 (mm) outliers start: 162 outliers final: 78 residues processed: 746 average time/residue: 0.2060 time to fit residues: 267.4515 Evaluate side-chains 676 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 578 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 501 optimal weight: 0.8980 chunk 417 optimal weight: 9.9990 chunk 409 optimal weight: 8.9990 chunk 451 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 397 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 456 optimal weight: 0.5980 chunk 170 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 466 HIS A 851 ASN A1179 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN C 466 HIS C 851 ASN C1252 GLN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.109085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.087034 restraints weight = 116878.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.090290 restraints weight = 62467.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092645 restraints weight = 40328.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.094225 restraints weight = 29080.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.095354 restraints weight = 23000.084| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41504 Z= 0.141 Angle : 0.790 23.584 56478 Z= 0.374 Chirality : 0.048 0.357 6514 Planarity : 0.005 0.059 7202 Dihedral : 7.015 58.756 6302 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.28 % Favored : 90.49 % Rotamer: Outliers : 3.71 % Allowed : 20.00 % Favored : 76.29 % 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: -2.22 (0.11), residues: 5110 helix: 0.99 (0.18), residues: 858 sheet: -0.96 (0.12), residues: 1784 loop : -2.86 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 270 TYR 0.042 0.002 TYR D1007 PHE 0.028 0.002 PHE A 114 TRP 0.014 0.001 TRP A 436 HIS 0.007 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00313 (41420) covalent geometry : angle 0.76434 (56270) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.76439 ( 88) hydrogen bonds : bond 0.04775 ( 540) hydrogen bonds : angle 5.04039 ( 1620) link_BETA1-4 : bond 0.00538 ( 12) link_BETA1-4 : angle 2.70123 ( 36) link_NAG-ASN : bond 0.00765 ( 28) link_NAG-ASN : angle 4.65327 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 594 time to evaluate : 1.510 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: A 66 SER cc_start: 0.8718 (t) cc_final: 0.7874 (p) REVERT: A 318 MET cc_start: 0.5129 (tpt) cc_final: 0.4897 (tpt) REVERT: A 384 ILE cc_start: 0.9539 (pt) cc_final: 0.9110 (mm) REVERT: A 456 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8772 (mmmm) REVERT: A 561 GLU cc_start: 0.6865 (pt0) cc_final: 0.6536 (pt0) REVERT: A 656 THR cc_start: -0.2176 (OUTLIER) cc_final: -0.2606 (p) REVERT: A 672 ASP cc_start: 0.8544 (t0) cc_final: 0.8276 (t0) REVERT: A 688 MET cc_start: 0.8746 (ppp) cc_final: 0.8438 (ppp) REVERT: A 778 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6962 (pt) REVERT: A 965 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8137 (mm) REVERT: A 988 ASP cc_start: 0.8958 (m-30) cc_final: 0.8557 (m-30) REVERT: A 1109 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8982 (mm) REVERT: A 1149 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9337 (tt) REVERT: A 1161 ASP cc_start: 0.8923 (p0) cc_final: 0.8588 (p0) REVERT: A 1165 GLU cc_start: 0.9164 (tt0) cc_final: 0.8875 (tt0) REVERT: A 1217 LEU cc_start: 0.9601 (mm) cc_final: 0.9389 (mm) REVERT: A 1314 MET cc_start: 0.8790 (mpp) cc_final: 0.8252 (mpp) REVERT: B 74 PHE cc_start: 0.8510 (t80) cc_final: 0.8106 (t80) REVERT: B 134 ASP cc_start: 0.8225 (t0) cc_final: 0.7848 (t70) REVERT: B 208 GLN cc_start: 0.7916 (tt0) cc_final: 0.7680 (tp-100) REVERT: B 222 GLU cc_start: 0.8403 (pt0) cc_final: 0.8080 (pp20) REVERT: B 253 LEU cc_start: 0.8751 (mm) cc_final: 0.8311 (pp) REVERT: B 318 MET cc_start: 0.5643 (mmm) cc_final: 0.5031 (tpt) REVERT: B 373 ASP cc_start: 0.8210 (p0) cc_final: 0.7878 (t0) REVERT: B 387 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7544 (ttm-80) REVERT: B 520 MET cc_start: 0.7394 (tmm) cc_final: 0.7058 (tmm) REVERT: B 561 GLU cc_start: 0.7294 (pt0) cc_final: 0.6825 (pt0) REVERT: B 578 LEU cc_start: 0.8307 (mt) cc_final: 0.7776 (pp) REVERT: B 605 LEU cc_start: 0.8455 (tp) cc_final: 0.8050 (tp) REVERT: B 669 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8581 (t80) REVERT: B 672 ASP cc_start: 0.8795 (t0) cc_final: 0.8531 (t0) REVERT: B 673 MET cc_start: 0.8561 (tpp) cc_final: 0.8137 (tpp) REVERT: B 688 MET cc_start: 0.8295 (ppp) cc_final: 0.8038 (ppp) REVERT: B 741 TRP cc_start: 0.8268 (t-100) cc_final: 0.7607 (t-100) REVERT: B 782 SER cc_start: 0.8061 (t) cc_final: 0.7811 (m) REVERT: B 786 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7017 (tt) REVERT: B 858 TRP cc_start: 0.7553 (m-90) cc_final: 0.7060 (m-90) REVERT: B 965 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7759 (mm) REVERT: B 977 MET cc_start: 0.9194 (mmm) cc_final: 0.8749 (mmm) REVERT: B 1018 TYR cc_start: 0.7968 (m-80) cc_final: 0.7685 (m-80) REVERT: B 1161 ASP cc_start: 0.8923 (p0) cc_final: 0.8546 (p0) REVERT: B 1172 GLU cc_start: 0.8992 (tt0) cc_final: 0.8204 (tm-30) REVERT: B 1217 LEU cc_start: 0.9335 (mm) cc_final: 0.9091 (mm) REVERT: C 66 SER cc_start: 0.8739 (t) cc_final: 0.7952 (p) REVERT: C 169 ASP cc_start: 0.6195 (m-30) cc_final: 0.5922 (m-30) REVERT: C 245 GLU cc_start: 0.8660 (pp20) cc_final: 0.8083 (pp20) REVERT: C 384 ILE cc_start: 0.9539 (pt) cc_final: 0.9071 (mm) REVERT: C 456 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8654 (mmmm) REVERT: C 656 THR cc_start: -0.2090 (OUTLIER) cc_final: -0.2484 (p) REVERT: C 666 MET cc_start: 0.8221 (tpp) cc_final: 0.8000 (tpp) REVERT: C 672 ASP cc_start: 0.8544 (t0) cc_final: 0.8267 (t0) REVERT: C 688 MET cc_start: 0.8765 (ppp) cc_final: 0.8416 (ppp) REVERT: C 778 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7013 (pt) REVERT: C 965 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 977 MET cc_start: 0.9234 (mmm) cc_final: 0.8993 (mmm) REVERT: C 988 ASP cc_start: 0.8938 (m-30) cc_final: 0.8550 (m-30) REVERT: C 1015 GLN cc_start: 0.8410 (tp40) cc_final: 0.8113 (tp40) REVERT: C 1109 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9016 (mm) REVERT: C 1149 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9334 (tt) REVERT: C 1161 ASP cc_start: 0.8912 (p0) cc_final: 0.8591 (p0) REVERT: C 1165 GLU cc_start: 0.9157 (tt0) cc_final: 0.8862 (tt0) REVERT: C 1217 LEU cc_start: 0.9613 (mm) cc_final: 0.9382 (mm) REVERT: C 1305 LEU cc_start: 0.8152 (mt) cc_final: 0.7935 (mp) REVERT: C 1314 MET cc_start: 0.8803 (mpp) cc_final: 0.8291 (mpp) REVERT: D 74 PHE cc_start: 0.8460 (t80) cc_final: 0.8084 (t80) REVERT: D 134 ASP cc_start: 0.8230 (t0) cc_final: 0.7837 (t70) REVERT: D 222 GLU cc_start: 0.8400 (pt0) cc_final: 0.8068 (pp20) REVERT: D 318 MET cc_start: 0.5610 (mmm) cc_final: 0.5008 (tpt) REVERT: D 372 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7904 (p) REVERT: D 387 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7524 (ttm-80) REVERT: D 500 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6480 (ttt) REVERT: D 520 MET cc_start: 0.7438 (tmm) cc_final: 0.7105 (tmm) REVERT: D 561 GLU cc_start: 0.7227 (pt0) cc_final: 0.6757 (pt0) REVERT: D 578 LEU cc_start: 0.8284 (mt) cc_final: 0.7752 (pp) REVERT: D 605 LEU cc_start: 0.8471 (tp) cc_final: 0.8081 (tp) REVERT: D 669 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8557 (t80) REVERT: D 672 ASP cc_start: 0.8760 (t0) cc_final: 0.8485 (m-30) REVERT: D 673 MET cc_start: 0.8479 (tpp) cc_final: 0.7960 (tpp) REVERT: D 688 MET cc_start: 0.8280 (ppp) cc_final: 0.7886 (ppp) REVERT: D 741 TRP cc_start: 0.8280 (t-100) cc_final: 0.7605 (t-100) REVERT: D 782 SER cc_start: 0.8012 (t) cc_final: 0.7770 (m) REVERT: D 786 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7072 (tt) REVERT: D 858 TRP cc_start: 0.7542 (m-90) cc_final: 0.7082 (m-90) REVERT: D 965 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7128 (mm) REVERT: D 977 MET cc_start: 0.9272 (mmm) cc_final: 0.8601 (mmm) REVERT: D 1015 GLN cc_start: 0.8727 (tp40) cc_final: 0.8223 (tp40) REVERT: D 1018 TYR cc_start: 0.7951 (m-80) cc_final: 0.7698 (m-10) REVERT: D 1035 ASN cc_start: 0.7903 (m-40) cc_final: 0.7632 (m-40) REVERT: D 1149 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9309 (tt) REVERT: D 1161 ASP cc_start: 0.8930 (p0) cc_final: 0.8557 (p0) REVERT: D 1217 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9087 (mm) outliers start: 166 outliers final: 94 residues processed: 714 average time/residue: 0.2079 time to fit residues: 256.2893 Evaluate side-chains 665 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 551 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 49 optimal weight: 8.9990 chunk 445 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 384 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 419 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A1015 GLN A1179 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN C1072 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.108641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.087312 restraints weight = 117293.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.090410 restraints weight = 62643.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092592 restraints weight = 40570.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.094046 restraints weight = 29569.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.095091 restraints weight = 23630.400| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 41504 Z= 0.163 Angle : 0.791 19.454 56478 Z= 0.378 Chirality : 0.048 0.354 6514 Planarity : 0.005 0.057 7202 Dihedral : 6.993 58.771 6302 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.30 % Favored : 90.51 % Rotamer: Outliers : 3.80 % Allowed : 20.89 % Favored : 75.30 % 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: -2.14 (0.12), residues: 5110 helix: 0.93 (0.18), residues: 864 sheet: -0.90 (0.12), residues: 1782 loop : -2.78 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.047 0.002 TYR B1007 PHE 0.029 0.002 PHE C 114 TRP 0.023 0.002 TRP B1237 HIS 0.007 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00363 (41420) covalent geometry : angle 0.76941 (56270) SS BOND : bond 0.00472 ( 44) SS BOND : angle 1.90672 ( 88) hydrogen bonds : bond 0.04864 ( 540) hydrogen bonds : angle 5.07433 ( 1620) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 2.63894 ( 36) link_NAG-ASN : bond 0.00755 ( 28) link_NAG-ASN : angle 4.10757 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 582 time to evaluate : 1.533 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: A 66 SER cc_start: 0.8841 (t) cc_final: 0.8126 (p) REVERT: A 310 GLN cc_start: 0.8332 (mp10) cc_final: 0.8004 (mp10) REVERT: A 318 MET cc_start: 0.5380 (tpt) cc_final: 0.5075 (tpt) REVERT: A 384 ILE cc_start: 0.9495 (pt) cc_final: 0.9062 (mm) REVERT: A 456 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8681 (mmmm) REVERT: A 567 LYS cc_start: 0.8364 (tppt) cc_final: 0.8102 (tppt) REVERT: A 656 THR cc_start: -0.1829 (OUTLIER) cc_final: -0.2247 (p) REVERT: A 672 ASP cc_start: 0.8517 (t0) cc_final: 0.8283 (t0) REVERT: A 778 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7167 (pt) REVERT: A 968 MET cc_start: 0.8197 (tpt) cc_final: 0.7512 (pmm) REVERT: A 988 ASP cc_start: 0.8931 (m-30) cc_final: 0.8511 (m-30) REVERT: A 1109 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9052 (mm) REVERT: A 1149 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9363 (tt) REVERT: A 1161 ASP cc_start: 0.8886 (p0) cc_final: 0.8572 (p0) REVERT: A 1165 GLU cc_start: 0.9112 (tt0) cc_final: 0.8821 (tt0) REVERT: A 1217 LEU cc_start: 0.9588 (mm) cc_final: 0.9386 (mm) REVERT: A 1314 MET cc_start: 0.8737 (mpp) cc_final: 0.8243 (mpp) REVERT: B 74 PHE cc_start: 0.8420 (t80) cc_final: 0.8057 (t80) REVERT: B 169 ASP cc_start: 0.6683 (t0) cc_final: 0.6447 (t70) REVERT: B 318 MET cc_start: 0.5730 (mmm) cc_final: 0.5081 (tpt) REVERT: B 373 ASP cc_start: 0.8096 (p0) cc_final: 0.7882 (t0) REVERT: B 387 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7792 (ttm-80) REVERT: B 561 GLU cc_start: 0.7374 (pt0) cc_final: 0.6960 (pt0) REVERT: B 578 LEU cc_start: 0.8272 (mt) cc_final: 0.7763 (pp) REVERT: B 605 LEU cc_start: 0.8312 (tp) cc_final: 0.8013 (tp) REVERT: B 669 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8559 (t80) REVERT: B 672 ASP cc_start: 0.8760 (t0) cc_final: 0.8436 (t0) REVERT: B 782 SER cc_start: 0.8015 (t) cc_final: 0.7802 (m) REVERT: B 858 TRP cc_start: 0.7553 (m-90) cc_final: 0.7070 (m-90) REVERT: B 977 MET cc_start: 0.9123 (mmm) cc_final: 0.8679 (mmm) REVERT: B 1018 TYR cc_start: 0.7941 (m-80) cc_final: 0.7709 (m-80) REVERT: B 1161 ASP cc_start: 0.8912 (p0) cc_final: 0.8525 (p0) REVERT: B 1172 GLU cc_start: 0.8987 (tt0) cc_final: 0.8190 (tm-30) REVERT: B 1217 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9141 (mm) REVERT: C 66 SER cc_start: 0.8825 (t) cc_final: 0.8116 (p) REVERT: C 245 GLU cc_start: 0.8625 (pp20) cc_final: 0.8078 (pp20) REVERT: C 310 GLN cc_start: 0.8316 (mp10) cc_final: 0.7998 (mp10) REVERT: C 384 ILE cc_start: 0.9515 (pt) cc_final: 0.9035 (mm) REVERT: C 456 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8805 (mmmm) REVERT: C 567 LYS cc_start: 0.8364 (tppt) cc_final: 0.8103 (tppt) REVERT: C 656 THR cc_start: -0.1992 (OUTLIER) cc_final: -0.2909 (p) REVERT: C 672 ASP cc_start: 0.8513 (t0) cc_final: 0.8230 (t0) REVERT: C 673 MET cc_start: 0.8883 (tpp) cc_final: 0.8673 (tpp) REVERT: C 959 MET cc_start: 0.8032 (ppp) cc_final: 0.7596 (pmm) REVERT: C 988 ASP cc_start: 0.8909 (m-30) cc_final: 0.8511 (m-30) REVERT: C 1015 GLN cc_start: 0.8482 (tp40) cc_final: 0.8278 (tp40) REVERT: C 1109 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9071 (mm) REVERT: C 1149 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9283 (tp) REVERT: C 1161 ASP cc_start: 0.8852 (p0) cc_final: 0.8529 (p0) REVERT: C 1165 GLU cc_start: 0.9095 (tt0) cc_final: 0.8810 (tt0) REVERT: C 1217 LEU cc_start: 0.9592 (mm) cc_final: 0.9371 (mm) REVERT: C 1305 LEU cc_start: 0.8199 (mt) cc_final: 0.7980 (mp) REVERT: C 1314 MET cc_start: 0.8745 (mpp) cc_final: 0.8220 (mpp) REVERT: D 74 PHE cc_start: 0.8400 (t80) cc_final: 0.8100 (t80) REVERT: D 253 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7649 (pp) REVERT: D 318 MET cc_start: 0.5729 (mmm) cc_final: 0.5097 (tpt) REVERT: D 387 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7823 (ttm-80) REVERT: D 500 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6542 (ttt) REVERT: D 520 MET cc_start: 0.7458 (tmm) cc_final: 0.7162 (tmm) REVERT: D 541 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6381 (pt) REVERT: D 561 GLU cc_start: 0.7356 (pt0) cc_final: 0.6904 (pt0) REVERT: D 578 LEU cc_start: 0.8281 (mt) cc_final: 0.7770 (pp) REVERT: D 605 LEU cc_start: 0.8384 (tp) cc_final: 0.8093 (tp) REVERT: D 669 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (t80) REVERT: D 673 MET cc_start: 0.8449 (tpp) cc_final: 0.7966 (tpp) REVERT: D 688 MET cc_start: 0.8217 (ppp) cc_final: 0.7965 (ppp) REVERT: D 782 SER cc_start: 0.8007 (t) cc_final: 0.7796 (m) REVERT: D 786 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7269 (tt) REVERT: D 858 TRP cc_start: 0.7488 (m-90) cc_final: 0.6988 (m-90) REVERT: D 965 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7358 (mm) REVERT: D 977 MET cc_start: 0.9176 (mmm) cc_final: 0.8583 (mmm) REVERT: D 1015 GLN cc_start: 0.8763 (tp40) cc_final: 0.8277 (tp40) REVERT: D 1035 ASN cc_start: 0.7896 (m-40) cc_final: 0.7670 (m110) REVERT: D 1149 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9348 (tt) REVERT: D 1161 ASP cc_start: 0.8938 (p0) cc_final: 0.8578 (p0) REVERT: D 1217 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9147 (mm) outliers start: 170 outliers final: 110 residues processed: 705 average time/residue: 0.1991 time to fit residues: 245.0567 Evaluate side-chains 678 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 551 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 503 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 448 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 422 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS A 644 ASN A 983 ASN A1179 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 HIS C 644 ASN C 967 GLN C1179 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.106185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084849 restraints weight = 117877.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.087831 restraints weight = 63487.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.089937 restraints weight = 41616.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.091381 restraints weight = 30555.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092311 restraints weight = 24514.195| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 41504 Z= 0.207 Angle : 0.821 15.072 56478 Z= 0.396 Chirality : 0.049 0.348 6514 Planarity : 0.005 0.058 7202 Dihedral : 7.156 58.953 6302 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.06 % Favored : 89.75 % Rotamer: Outliers : 3.62 % Allowed : 22.17 % Favored : 74.21 % 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: -2.15 (0.12), residues: 5110 helix: 0.85 (0.17), residues: 872 sheet: -0.92 (0.12), residues: 1788 loop : -2.75 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 360 TYR 0.042 0.002 TYR D1007 PHE 0.026 0.002 PHE C 114 TRP 0.017 0.002 TRP C 436 HIS 0.006 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00453 (41420) covalent geometry : angle 0.80320 (56270) SS BOND : bond 0.00340 ( 44) SS BOND : angle 1.91914 ( 88) hydrogen bonds : bond 0.04976 ( 540) hydrogen bonds : angle 5.19607 ( 1620) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 2.65050 ( 36) link_NAG-ASN : bond 0.00747 ( 28) link_NAG-ASN : angle 3.69724 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 568 time to evaluate : 1.246 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: A 66 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8514 (p) REVERT: A 216 GLU cc_start: 0.8078 (mp0) cc_final: 0.7833 (mp0) REVERT: A 310 GLN cc_start: 0.8475 (mp10) cc_final: 0.8106 (mp10) REVERT: A 318 MET cc_start: 0.5549 (tpt) cc_final: 0.5184 (tpt) REVERT: A 384 ILE cc_start: 0.9537 (pt) cc_final: 0.9108 (mm) REVERT: A 456 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8753 (mmmm) REVERT: A 567 LYS cc_start: 0.8353 (tppt) cc_final: 0.8094 (tppt) REVERT: A 582 HIS cc_start: 0.7184 (t70) cc_final: 0.6904 (t70) REVERT: A 656 THR cc_start: -0.1993 (OUTLIER) cc_final: -0.2440 (p) REVERT: A 672 ASP cc_start: 0.8612 (t0) cc_final: 0.8340 (t0) REVERT: A 673 MET cc_start: 0.8901 (tpp) cc_final: 0.8639 (tpp) REVERT: A 687 LYS cc_start: 0.9120 (tttt) cc_final: 0.8632 (tptp) REVERT: A 968 MET cc_start: 0.8242 (tpt) cc_final: 0.7141 (pmm) REVERT: A 988 ASP cc_start: 0.8971 (m-30) cc_final: 0.8563 (m-30) REVERT: A 1074 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8408 (tp-100) REVERT: A 1109 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9082 (mm) REVERT: A 1149 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9414 (tt) REVERT: A 1161 ASP cc_start: 0.8941 (p0) cc_final: 0.8618 (p0) REVERT: A 1165 GLU cc_start: 0.9144 (tt0) cc_final: 0.8856 (tt0) REVERT: A 1208 MET cc_start: 0.9158 (ppp) cc_final: 0.8783 (ppp) REVERT: A 1217 LEU cc_start: 0.9610 (mm) cc_final: 0.9407 (mm) REVERT: A 1314 MET cc_start: 0.8763 (mpp) cc_final: 0.8156 (mpp) REVERT: B 74 PHE cc_start: 0.8464 (t80) cc_final: 0.8187 (t80) REVERT: B 121 MET cc_start: 0.8176 (ttm) cc_final: 0.7892 (tpp) REVERT: B 253 LEU cc_start: 0.8501 (mm) cc_final: 0.7971 (mm) REVERT: B 318 MET cc_start: 0.5658 (mmm) cc_final: 0.5188 (tpt) REVERT: B 373 ASP cc_start: 0.8211 (p0) cc_final: 0.7968 (t0) REVERT: B 387 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7769 (ttm-80) REVERT: B 561 GLU cc_start: 0.7451 (pt0) cc_final: 0.7010 (pt0) REVERT: B 578 LEU cc_start: 0.8435 (mt) cc_final: 0.7955 (pp) REVERT: B 605 LEU cc_start: 0.8471 (tp) cc_final: 0.8148 (tp) REVERT: B 669 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8586 (t80) REVERT: B 672 ASP cc_start: 0.8793 (t0) cc_final: 0.8551 (t0) REVERT: B 782 SER cc_start: 0.8108 (t) cc_final: 0.7872 (m) REVERT: B 811 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7891 (mmtm) REVERT: B 977 MET cc_start: 0.9169 (mmm) cc_final: 0.8628 (mmm) REVERT: B 1161 ASP cc_start: 0.8959 (p0) cc_final: 0.8652 (p0) REVERT: B 1172 GLU cc_start: 0.9043 (tt0) cc_final: 0.8177 (tm-30) REVERT: B 1217 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9206 (mm) REVERT: C 66 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8548 (p) REVERT: C 216 GLU cc_start: 0.8072 (mp0) cc_final: 0.7842 (mp0) REVERT: C 245 GLU cc_start: 0.8648 (pp20) cc_final: 0.8076 (pp20) REVERT: C 310 GLN cc_start: 0.8453 (mp10) cc_final: 0.8096 (mp10) REVERT: C 318 MET cc_start: 0.5542 (tpt) cc_final: 0.5268 (tpt) REVERT: C 384 ILE cc_start: 0.9559 (pt) cc_final: 0.9089 (mm) REVERT: C 456 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8916 (mmmm) REVERT: C 567 LYS cc_start: 0.8346 (tppt) cc_final: 0.8089 (tppt) REVERT: C 582 HIS cc_start: 0.7217 (t70) cc_final: 0.6941 (t70) REVERT: C 656 THR cc_start: -0.2644 (OUTLIER) cc_final: -0.2986 (p) REVERT: C 672 ASP cc_start: 0.8591 (t0) cc_final: 0.8291 (t0) REVERT: C 687 LYS cc_start: 0.9114 (tttt) cc_final: 0.8605 (tptt) REVERT: C 988 ASP cc_start: 0.8888 (m-30) cc_final: 0.8504 (m-30) REVERT: C 1109 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9093 (mm) REVERT: C 1149 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9307 (tp) REVERT: C 1161 ASP cc_start: 0.8945 (p0) cc_final: 0.8640 (p0) REVERT: C 1165 GLU cc_start: 0.9146 (tt0) cc_final: 0.8852 (tt0) REVERT: C 1208 MET cc_start: 0.9144 (ppp) cc_final: 0.8761 (ppp) REVERT: C 1217 LEU cc_start: 0.9621 (mm) cc_final: 0.9391 (mm) REVERT: C 1314 MET cc_start: 0.8776 (mpp) cc_final: 0.8186 (mpp) REVERT: D 74 PHE cc_start: 0.8438 (t80) cc_final: 0.8118 (t80) REVERT: D 318 MET cc_start: 0.5711 (mmm) cc_final: 0.5327 (mmm) REVERT: D 387 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7814 (ttm-80) REVERT: D 441 HIS cc_start: 0.6765 (OUTLIER) cc_final: 0.6510 (t-170) REVERT: D 500 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6601 (ttt) REVERT: D 520 MET cc_start: 0.7701 (tmm) cc_final: 0.7365 (tmm) REVERT: D 541 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6377 (pt) REVERT: D 561 GLU cc_start: 0.7411 (pt0) cc_final: 0.6961 (pt0) REVERT: D 578 LEU cc_start: 0.8449 (mt) cc_final: 0.7963 (pp) REVERT: D 605 LEU cc_start: 0.8461 (tp) cc_final: 0.8146 (tp) REVERT: D 613 LEU cc_start: 0.6447 (tp) cc_final: 0.6228 (tp) REVERT: D 669 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8656 (t80) REVERT: D 673 MET cc_start: 0.8606 (tpp) cc_final: 0.8071 (tpp) REVERT: D 688 MET cc_start: 0.8188 (ppp) cc_final: 0.7928 (ppp) REVERT: D 782 SER cc_start: 0.8085 (t) cc_final: 0.7870 (m) REVERT: D 811 LYS cc_start: 0.8258 (mmtp) cc_final: 0.7858 (mmtm) REVERT: D 965 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7544 (mm) REVERT: D 1035 ASN cc_start: 0.7919 (m-40) cc_final: 0.7539 (m110) REVERT: D 1149 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9380 (tt) REVERT: D 1161 ASP cc_start: 0.8935 (p0) cc_final: 0.8634 (p0) REVERT: D 1217 LEU cc_start: 0.9411 (mm) cc_final: 0.9211 (mm) outliers start: 162 outliers final: 115 residues processed: 694 average time/residue: 0.2015 time to fit residues: 242.4916 Evaluate side-chains 668 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 536 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1074 GLN Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1035 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 120 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 465 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 172 optimal weight: 0.0040 chunk 351 optimal weight: 10.0000 chunk 438 optimal weight: 7.9990 chunk 490 optimal weight: 0.8980 chunk 464 optimal weight: 7.9990 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.104608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083003 restraints weight = 116795.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.086041 restraints weight = 62634.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088127 restraints weight = 40695.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089555 restraints weight = 29906.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.090508 restraints weight = 24024.479| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 41504 Z= 0.226 Angle : 0.835 17.031 56478 Z= 0.405 Chirality : 0.049 0.347 6514 Planarity : 0.005 0.058 7202 Dihedral : 7.299 59.343 6302 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.86 % Favored : 89.94 % Rotamer: Outliers : 3.74 % Allowed : 22.64 % Favored : 73.62 % 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: -2.21 (0.12), residues: 5110 helix: 0.80 (0.17), residues: 872 sheet: -0.98 (0.12), residues: 1766 loop : -2.76 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.034 0.002 TYR D1007 PHE 0.033 0.002 PHE C 192 TRP 0.036 0.002 TRP B1237 HIS 0.038 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00492 (41420) covalent geometry : angle 0.81951 (56270) SS BOND : bond 0.00347 ( 44) SS BOND : angle 1.87277 ( 88) hydrogen bonds : bond 0.05210 ( 540) hydrogen bonds : angle 5.29311 ( 1620) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 2.65651 ( 36) link_NAG-ASN : bond 0.00711 ( 28) link_NAG-ASN : angle 3.52799 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 557 time to evaluate : 1.573 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: A 66 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 216 GLU cc_start: 0.8088 (mp0) cc_final: 0.7840 (mp0) REVERT: A 384 ILE cc_start: 0.9551 (pt) cc_final: 0.9185 (mm) REVERT: A 456 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8952 (mmmm) REVERT: A 567 LYS cc_start: 0.8421 (tppt) cc_final: 0.8194 (tppt) REVERT: A 582 HIS cc_start: 0.7264 (t70) cc_final: 0.7031 (t70) REVERT: A 656 THR cc_start: -0.1843 (OUTLIER) cc_final: -0.2317 (p) REVERT: A 851 ASN cc_start: 0.9050 (m-40) cc_final: 0.8371 (m110) REVERT: A 968 MET cc_start: 0.8231 (tpt) cc_final: 0.7348 (pmm) REVERT: A 988 ASP cc_start: 0.9015 (m-30) cc_final: 0.8623 (m-30) REVERT: A 1018 TYR cc_start: 0.8287 (m-80) cc_final: 0.7812 (t80) REVERT: A 1074 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8434 (tp-100) REVERT: A 1109 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9093 (mm) REVERT: A 1149 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9427 (tt) REVERT: A 1161 ASP cc_start: 0.8961 (p0) cc_final: 0.8654 (p0) REVERT: A 1165 GLU cc_start: 0.9177 (tt0) cc_final: 0.8884 (tt0) REVERT: A 1314 MET cc_start: 0.8733 (mpp) cc_final: 0.8109 (mpp) REVERT: B 74 PHE cc_start: 0.8510 (t80) cc_final: 0.8244 (t80) REVERT: B 121 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7923 (tpp) REVERT: B 318 MET cc_start: 0.5947 (mmm) cc_final: 0.5532 (mmm) REVERT: B 373 ASP cc_start: 0.8270 (p0) cc_final: 0.7983 (t0) REVERT: B 387 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7799 (ttm-80) REVERT: B 464 MET cc_start: 0.7541 (ttt) cc_final: 0.7315 (ttt) REVERT: B 561 GLU cc_start: 0.7511 (pt0) cc_final: 0.7062 (pt0) REVERT: B 578 LEU cc_start: 0.8453 (mt) cc_final: 0.7955 (pp) REVERT: B 579 PRO cc_start: 0.7685 (Cg_exo) cc_final: 0.7395 (Cg_exo) REVERT: B 605 LEU cc_start: 0.8435 (tp) cc_final: 0.8052 (tp) REVERT: B 669 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8689 (t80) REVERT: B 672 ASP cc_start: 0.8789 (t0) cc_final: 0.8514 (t0) REVERT: B 782 SER cc_start: 0.8127 (t) cc_final: 0.7905 (m) REVERT: B 811 LYS cc_start: 0.8309 (mmtp) cc_final: 0.7895 (mmtm) REVERT: B 977 MET cc_start: 0.9210 (mmm) cc_final: 0.8676 (mmm) REVERT: B 1161 ASP cc_start: 0.9015 (p0) cc_final: 0.8743 (p0) REVERT: B 1172 GLU cc_start: 0.9062 (tt0) cc_final: 0.8173 (tm-30) REVERT: B 1217 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9225 (mm) REVERT: C 66 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8623 (p) REVERT: C 199 PHE cc_start: 0.7962 (m-80) cc_final: 0.7754 (m-80) REVERT: C 216 GLU cc_start: 0.8075 (mp0) cc_final: 0.7859 (mp0) REVERT: C 318 MET cc_start: 0.5794 (tpt) cc_final: 0.5540 (tpt) REVERT: C 384 ILE cc_start: 0.9569 (pt) cc_final: 0.9122 (mm) REVERT: C 456 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8949 (mmmm) REVERT: C 567 LYS cc_start: 0.8417 (tppt) cc_final: 0.8198 (tppt) REVERT: C 582 HIS cc_start: 0.7273 (t70) cc_final: 0.7045 (t70) REVERT: C 656 THR cc_start: -0.2562 (OUTLIER) cc_final: -0.2905 (p) REVERT: C 851 ASN cc_start: 0.8867 (t0) cc_final: 0.8430 (m-40) REVERT: C 988 ASP cc_start: 0.8856 (m-30) cc_final: 0.8498 (m-30) REVERT: C 999 GLU cc_start: 0.8532 (pp20) cc_final: 0.8252 (tm-30) REVERT: C 1074 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8240 (tp40) REVERT: C 1109 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9101 (mm) REVERT: C 1149 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9330 (tp) REVERT: C 1161 ASP cc_start: 0.8981 (p0) cc_final: 0.8681 (p0) REVERT: C 1165 GLU cc_start: 0.9168 (tt0) cc_final: 0.8875 (tt0) REVERT: C 1217 LEU cc_start: 0.9631 (mm) cc_final: 0.9410 (mm) REVERT: C 1314 MET cc_start: 0.8740 (mpp) cc_final: 0.8070 (mpp) REVERT: D 74 PHE cc_start: 0.8472 (t80) cc_final: 0.8185 (t80) REVERT: D 169 ASP cc_start: 0.6923 (t0) cc_final: 0.6705 (t0) REVERT: D 318 MET cc_start: 0.5944 (mmm) cc_final: 0.5523 (tpt) REVERT: D 464 MET cc_start: 0.7624 (ttt) cc_final: 0.7375 (ttt) REVERT: D 500 MET cc_start: 0.7107 (ttt) cc_final: 0.6788 (ttt) REVERT: D 520 MET cc_start: 0.7663 (tmm) cc_final: 0.7388 (tmm) REVERT: D 541 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6263 (pt) REVERT: D 561 GLU cc_start: 0.7464 (pt0) cc_final: 0.7052 (pt0) REVERT: D 578 LEU cc_start: 0.8467 (mt) cc_final: 0.7971 (pp) REVERT: D 579 PRO cc_start: 0.7671 (Cg_exo) cc_final: 0.7376 (Cg_exo) REVERT: D 605 LEU cc_start: 0.8430 (tp) cc_final: 0.8057 (tp) REVERT: D 656 THR cc_start: -0.1493 (OUTLIER) cc_final: -0.1797 (t) REVERT: D 669 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8736 (t80) REVERT: D 673 MET cc_start: 0.8708 (tpp) cc_final: 0.8173 (tpp) REVERT: D 688 MET cc_start: 0.8238 (ppp) cc_final: 0.7971 (ppp) REVERT: D 770 PHE cc_start: 0.8354 (t80) cc_final: 0.8122 (t80) REVERT: D 782 SER cc_start: 0.8123 (t) cc_final: 0.7880 (m) REVERT: D 811 LYS cc_start: 0.8325 (mmtp) cc_final: 0.7899 (mmtm) REVERT: D 965 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (mm) REVERT: D 977 MET cc_start: 0.9191 (mmm) cc_final: 0.8648 (mmm) REVERT: D 1035 ASN cc_start: 0.7978 (m-40) cc_final: 0.7551 (m110) REVERT: D 1149 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9388 (tt) REVERT: D 1161 ASP cc_start: 0.9000 (p0) cc_final: 0.8711 (p0) REVERT: D 1213 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9291 (tp) REVERT: D 1217 LEU cc_start: 0.9436 (mm) cc_final: 0.9218 (mm) REVERT: D 1298 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8585 (mt) outliers start: 167 outliers final: 125 residues processed: 683 average time/residue: 0.2070 time to fit residues: 245.7294 Evaluate side-chains 673 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 528 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1035 ASN Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1074 GLN Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 500 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1035 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1074 GLN Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1213 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1298 LEU Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 412 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 415 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 283 optimal weight: 8.9990 chunk 394 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS D 938 ASN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081288 restraints weight = 117217.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.084180 restraints weight = 62818.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086251 restraints weight = 41219.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.087680 restraints weight = 30311.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088691 restraints weight = 24279.976| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 41504 Z= 0.247 Angle : 0.867 16.001 56478 Z= 0.424 Chirality : 0.050 0.351 6514 Planarity : 0.005 0.080 7202 Dihedral : 7.537 64.117 6302 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.98 % Favored : 88.83 % Rotamer: Outliers : 3.74 % Allowed : 23.18 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.12), residues: 5110 helix: 0.61 (0.17), residues: 884 sheet: -1.10 (0.12), residues: 1736 loop : -2.75 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 684 TYR 0.039 0.002 TYR C 667 PHE 0.030 0.002 PHE A 458 TRP 0.019 0.002 TRP C 436 HIS 0.013 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00539 (41420) covalent geometry : angle 0.85302 (56270) SS BOND : bond 0.00375 ( 44) SS BOND : angle 1.87975 ( 88) hydrogen bonds : bond 0.05482 ( 540) hydrogen bonds : angle 5.30469 ( 1620) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 2.69565 ( 36) link_NAG-ASN : bond 0.00698 ( 28) link_NAG-ASN : angle 3.41756 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 539 time to evaluate : 1.394 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: A 66 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 216 GLU cc_start: 0.8048 (mp0) cc_final: 0.7817 (mp0) REVERT: A 246 MET cc_start: 0.6261 (mmt) cc_final: 0.5745 (mmt) REVERT: A 456 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8967 (mmmm) REVERT: A 567 LYS cc_start: 0.8487 (tppt) cc_final: 0.8249 (tppt) REVERT: A 851 ASN cc_start: 0.9000 (m-40) cc_final: 0.8350 (m110) REVERT: A 968 MET cc_start: 0.8216 (tpt) cc_final: 0.7629 (pmm) REVERT: A 988 ASP cc_start: 0.8875 (m-30) cc_final: 0.8443 (m-30) REVERT: A 1074 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8442 (tp-100) REVERT: A 1109 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 1149 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9456 (tt) REVERT: A 1161 ASP cc_start: 0.8995 (p0) cc_final: 0.8699 (p0) REVERT: A 1165 GLU cc_start: 0.9199 (tt0) cc_final: 0.8937 (tt0) REVERT: A 1314 MET cc_start: 0.8672 (mpp) cc_final: 0.8040 (mpp) REVERT: B 74 PHE cc_start: 0.8498 (t80) cc_final: 0.8263 (t80) REVERT: B 121 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7942 (tpp) REVERT: B 318 MET cc_start: 0.6124 (mmm) cc_final: 0.5593 (tpt) REVERT: B 373 ASP cc_start: 0.8347 (p0) cc_final: 0.7970 (t70) REVERT: B 464 MET cc_start: 0.7806 (ttt) cc_final: 0.7595 (ttt) REVERT: B 561 GLU cc_start: 0.7465 (pt0) cc_final: 0.7052 (pt0) REVERT: B 602 GLN cc_start: 0.7391 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 605 LEU cc_start: 0.8435 (tp) cc_final: 0.8213 (tp) REVERT: B 669 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8790 (t80) REVERT: B 672 ASP cc_start: 0.8797 (t0) cc_final: 0.8511 (t0) REVERT: B 782 SER cc_start: 0.8205 (t) cc_final: 0.7950 (m) REVERT: B 811 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7909 (mmtm) REVERT: B 878 GLU cc_start: 0.8695 (pm20) cc_final: 0.8384 (pm20) REVERT: B 977 MET cc_start: 0.9189 (mmm) cc_final: 0.8649 (mmm) REVERT: B 1147 LYS cc_start: 0.9113 (mttp) cc_final: 0.8570 (mttp) REVERT: B 1161 ASP cc_start: 0.9030 (p0) cc_final: 0.8825 (p0) REVERT: B 1172 GLU cc_start: 0.9088 (tt0) cc_final: 0.8167 (tm-30) REVERT: B 1217 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9241 (mm) REVERT: C 66 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8806 (p) REVERT: C 199 PHE cc_start: 0.7931 (m-80) cc_final: 0.7640 (m-80) REVERT: C 216 GLU cc_start: 0.8045 (mp0) cc_final: 0.7823 (mp0) REVERT: C 246 MET cc_start: 0.6472 (mmt) cc_final: 0.6090 (mmt) REVERT: C 318 MET cc_start: 0.5923 (tpt) cc_final: 0.5638 (tpt) REVERT: C 384 ILE cc_start: 0.9560 (pt) cc_final: 0.9165 (mm) REVERT: C 456 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8754 (mmmt) REVERT: C 567 LYS cc_start: 0.8482 (tppt) cc_final: 0.8241 (tppt) REVERT: C 665 ASP cc_start: 0.7858 (t0) cc_final: 0.7549 (t70) REVERT: C 851 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: C 999 GLU cc_start: 0.8573 (pp20) cc_final: 0.8307 (tm-30) REVERT: C 1018 TYR cc_start: 0.8293 (m-80) cc_final: 0.7895 (t80) REVERT: C 1109 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9099 (mm) REVERT: C 1149 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9388 (tp) REVERT: C 1161 ASP cc_start: 0.8995 (p0) cc_final: 0.8698 (p0) REVERT: C 1165 GLU cc_start: 0.9181 (tt0) cc_final: 0.8925 (tt0) REVERT: C 1217 LEU cc_start: 0.9625 (mm) cc_final: 0.9418 (mm) REVERT: C 1314 MET cc_start: 0.8699 (mpp) cc_final: 0.8038 (mpp) REVERT: D 74 PHE cc_start: 0.8480 (t80) cc_final: 0.8233 (t80) REVERT: D 169 ASP cc_start: 0.6939 (t0) cc_final: 0.6684 (t0) REVERT: D 318 MET cc_start: 0.6275 (mmm) cc_final: 0.5790 (tpt) REVERT: D 500 MET cc_start: 0.7449 (ttt) cc_final: 0.7147 (ttt) REVERT: D 520 MET cc_start: 0.7716 (tmm) cc_final: 0.7436 (tmm) REVERT: D 541 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6317 (pt) REVERT: D 561 GLU cc_start: 0.7412 (pt0) cc_final: 0.7036 (pt0) REVERT: D 602 GLN cc_start: 0.7363 (tm-30) cc_final: 0.6935 (tm-30) REVERT: D 605 LEU cc_start: 0.8429 (tp) cc_final: 0.8212 (tp) REVERT: D 669 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8736 (t80) REVERT: D 673 MET cc_start: 0.8823 (tpp) cc_final: 0.8397 (tpp) REVERT: D 688 MET cc_start: 0.8343 (ppp) cc_final: 0.8119 (ppp) REVERT: D 770 PHE cc_start: 0.8369 (t80) cc_final: 0.8164 (t80) REVERT: D 811 LYS cc_start: 0.8253 (mmtp) cc_final: 0.7866 (mmtm) REVERT: D 977 MET cc_start: 0.9219 (mmm) cc_final: 0.8678 (mmm) REVERT: D 1035 ASN cc_start: 0.8054 (m-40) cc_final: 0.7553 (m110) REVERT: D 1147 LYS cc_start: 0.9048 (mttp) cc_final: 0.8534 (mttp) REVERT: D 1149 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9393 (tt) REVERT: D 1161 ASP cc_start: 0.9024 (p0) cc_final: 0.8818 (p0) REVERT: D 1208 MET cc_start: 0.8795 (ppp) cc_final: 0.8574 (ppp) REVERT: D 1217 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9262 (mm) outliers start: 167 outliers final: 126 residues processed: 665 average time/residue: 0.2023 time to fit residues: 235.8099 Evaluate side-chains 654 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 513 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1035 ASN Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1074 GLN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1323 TYR Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 619 TYR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 851 ASN Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1035 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1298 LEU Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 301 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 425 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 432 optimal weight: 0.5980 chunk 160 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS B 938 ASN B 961 ASN B 983 ASN B 994 GLN B1242 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN D 132 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 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 = 0.3936 r_free = 0.3936 target = 0.106841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.085229 restraints weight = 114741.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088265 restraints weight = 61331.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090438 restraints weight = 39917.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.091931 restraints weight = 29128.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.092829 restraints weight = 23315.582| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41504 Z= 0.144 Angle : 0.834 17.027 56478 Z= 0.397 Chirality : 0.050 0.375 6514 Planarity : 0.005 0.062 7202 Dihedral : 7.312 71.561 6302 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.02 % Favored : 90.78 % Rotamer: Outliers : 2.71 % Allowed : 24.16 % Favored : 73.13 % 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: -2.15 (0.12), residues: 5110 helix: 0.84 (0.17), residues: 880 sheet: -1.01 (0.12), residues: 1772 loop : -2.67 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 853 TYR 0.034 0.002 TYR C 800 PHE 0.060 0.002 PHE A 114 TRP 0.019 0.001 TRP B1237 HIS 0.005 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00328 (41420) covalent geometry : angle 0.82127 (56270) SS BOND : bond 0.00288 ( 44) SS BOND : angle 1.62701 ( 88) hydrogen bonds : bond 0.05037 ( 540) hydrogen bonds : angle 4.95091 ( 1620) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 2.61901 ( 36) link_NAG-ASN : bond 0.00657 ( 28) link_NAG-ASN : angle 3.26616 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 591 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: A 66 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8805 (p) REVERT: A 216 GLU cc_start: 0.8009 (mp0) cc_final: 0.7776 (mp0) REVERT: A 246 MET cc_start: 0.6219 (mmt) cc_final: 0.5955 (mmt) REVERT: A 384 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8968 (mm) REVERT: A 456 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8829 (mmmm) REVERT: A 560 VAL cc_start: 0.7791 (t) cc_final: 0.7552 (t) REVERT: A 656 THR cc_start: -0.1923 (OUTLIER) cc_final: -0.2502 (p) REVERT: A 851 ASN cc_start: 0.9005 (m-40) cc_final: 0.8358 (m110) REVERT: A 988 ASP cc_start: 0.8800 (m-30) cc_final: 0.8352 (m-30) REVERT: A 1018 TYR cc_start: 0.8177 (m-80) cc_final: 0.7883 (t80) REVERT: A 1109 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9028 (mm) REVERT: A 1121 VAL cc_start: 0.8907 (m) cc_final: 0.8700 (p) REVERT: A 1149 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9365 (tt) REVERT: A 1161 ASP cc_start: 0.8887 (p0) cc_final: 0.8578 (p0) REVERT: A 1165 GLU cc_start: 0.9135 (tt0) cc_final: 0.8878 (tt0) REVERT: A 1314 MET cc_start: 0.8733 (mpp) cc_final: 0.8256 (mpp) REVERT: B 121 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7864 (tpp) REVERT: B 253 LEU cc_start: 0.8413 (mm) cc_final: 0.7943 (mm) REVERT: B 318 MET cc_start: 0.6176 (mmm) cc_final: 0.5617 (tpt) REVERT: B 541 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6735 (pt) REVERT: B 561 GLU cc_start: 0.7479 (pt0) cc_final: 0.7119 (pt0) REVERT: B 672 ASP cc_start: 0.8686 (t0) cc_final: 0.8393 (t0) REVERT: B 770 PHE cc_start: 0.8247 (t80) cc_final: 0.8028 (t80) REVERT: B 782 SER cc_start: 0.8011 (t) cc_final: 0.7790 (m) REVERT: B 811 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7865 (mmtm) REVERT: B 878 GLU cc_start: 0.8679 (pm20) cc_final: 0.8301 (pm20) REVERT: B 977 MET cc_start: 0.9071 (mmm) cc_final: 0.8484 (mmm) REVERT: B 1172 GLU cc_start: 0.9015 (tt0) cc_final: 0.8133 (tm-30) REVERT: B 1311 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: C 66 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8796 (p) REVERT: C 169 ASP cc_start: 0.6786 (m-30) cc_final: 0.6065 (m-30) REVERT: C 199 PHE cc_start: 0.7889 (m-80) cc_final: 0.7671 (m-80) REVERT: C 216 GLU cc_start: 0.7983 (mp0) cc_final: 0.7754 (mp0) REVERT: C 318 MET cc_start: 0.5932 (tpt) cc_final: 0.5700 (tpt) REVERT: C 384 ILE cc_start: 0.9473 (pt) cc_final: 0.9254 (mp) REVERT: C 456 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8893 (mmmm) REVERT: C 520 MET cc_start: 0.7975 (tmm) cc_final: 0.7766 (tmm) REVERT: C 560 VAL cc_start: 0.7812 (t) cc_final: 0.7587 (t) REVERT: C 656 THR cc_start: -0.2138 (OUTLIER) cc_final: -0.2541 (p) REVERT: C 851 ASN cc_start: 0.8634 (t0) cc_final: 0.8289 (m-40) REVERT: C 988 ASP cc_start: 0.8890 (m-30) cc_final: 0.8408 (m-30) REVERT: C 999 GLU cc_start: 0.8525 (pp20) cc_final: 0.8247 (tm-30) REVERT: C 1109 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9045 (mm) REVERT: C 1121 VAL cc_start: 0.8913 (m) cc_final: 0.8699 (p) REVERT: C 1149 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9337 (tp) REVERT: C 1161 ASP cc_start: 0.8889 (p0) cc_final: 0.8579 (p0) REVERT: C 1165 GLU cc_start: 0.9121 (tt0) cc_final: 0.8869 (tt0) REVERT: C 1217 LEU cc_start: 0.9557 (mm) cc_final: 0.9356 (mm) REVERT: C 1314 MET cc_start: 0.8722 (mpp) cc_final: 0.8252 (mpp) REVERT: D 74 PHE cc_start: 0.8389 (t80) cc_final: 0.8181 (t80) REVERT: D 169 ASP cc_start: 0.6561 (t0) cc_final: 0.6317 (t0) REVERT: D 253 LEU cc_start: 0.8083 (mt) cc_final: 0.7485 (pp) REVERT: D 318 MET cc_start: 0.6152 (mmm) cc_final: 0.5591 (tpt) REVERT: D 520 MET cc_start: 0.7699 (tmm) cc_final: 0.7494 (tmm) REVERT: D 541 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6446 (pt) REVERT: D 561 GLU cc_start: 0.7453 (pt0) cc_final: 0.7121 (pt0) REVERT: D 673 MET cc_start: 0.8635 (tpp) cc_final: 0.8177 (tpp) REVERT: D 782 SER cc_start: 0.8034 (t) cc_final: 0.7800 (m) REVERT: D 811 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7846 (mmtm) REVERT: D 977 MET cc_start: 0.9086 (mmm) cc_final: 0.8521 (mmm) REVERT: D 1035 ASN cc_start: 0.8020 (m-40) cc_final: 0.7649 (m110) REVERT: D 1149 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9315 (tt) REVERT: D 1237 TRP cc_start: 0.8050 (t60) cc_final: 0.7704 (t60) outliers start: 121 outliers final: 85 residues processed: 685 average time/residue: 0.2029 time to fit residues: 242.4439 Evaluate side-chains 632 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 533 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 983 ASN Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1311 GLU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 500 optimal weight: 3.9990 chunk 480 optimal weight: 0.7980 chunk 393 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 299 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 582 HIS A1252 GLN ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 582 HIS C 851 ASN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.106507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.085015 restraints weight = 116463.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.088072 restraints weight = 62050.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.090235 restraints weight = 40267.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.091693 restraints weight = 29378.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.092717 restraints weight = 23465.589| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 41504 Z= 0.216 Angle : 0.909 59.193 56478 Z= 0.455 Chirality : 0.052 0.790 6514 Planarity : 0.005 0.066 7202 Dihedral : 7.329 71.568 6302 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.14 % Favored : 90.65 % Rotamer: Outliers : 2.75 % Allowed : 24.50 % Favored : 72.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.14 (0.12), residues: 5110 helix: 0.80 (0.17), residues: 878 sheet: -0.98 (0.12), residues: 1742 loop : -2.65 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 68 TYR 0.074 0.002 TYR C1018 PHE 0.032 0.002 PHE B 669 TRP 0.016 0.001 TRP B1237 HIS 0.004 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00485 (41420) covalent geometry : angle 0.89660 (56270) SS BOND : bond 0.00344 ( 44) SS BOND : angle 1.62049 ( 88) hydrogen bonds : bond 0.05057 ( 540) hydrogen bonds : angle 4.91373 ( 1620) link_BETA1-4 : bond 0.00768 ( 12) link_BETA1-4 : angle 2.71004 ( 36) link_NAG-ASN : bond 0.00658 ( 28) link_NAG-ASN : angle 3.26111 ( 84) =============================================================================== Job complete usr+sys time: 7388.63 seconds wall clock time: 128 minutes 54.05 seconds (7734.05 seconds total)