Starting phenix.real_space_refine on Mon Jul 6 22:45:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o7q_12753/07_2026/7o7q_12753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7q_12753/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7o7q_12753/07_2026/7o7q_12753.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o7q_12753/07_2026/7o7q_12753.cif" model { file = "/net/cci-nas-00/data/ceres_data/7o7q_12753/07_2026/7o7q_12753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7q_12753/07_2026/7o7q_12753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7q_12753/07_2026/7o7q_12753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7q_12753/07_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): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.28, per 1000 atoms: 0.25 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: 3.58 Conformation dependent library (CDL) restraints added in 1.8 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: 0.83 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: 5.08 Time building geometry restraints manager: 4.73 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 - 18.04: 22139 18.04 - 36.07: 2060 36.07 - 54.11: 405 54.11 - 72.15: 98 72.15 - 90.18: 28 Dihedral angle restraints: 24730 sinusoidal: 9816 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 24727 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: 0.09 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.160 Process input model: 34.780 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 : 14.433 90.182 14998 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/Z covalent geometry : bond 0.00975 / 0.49 (41420) covalent geometry : angle 1.53776 / 0.89 (56270) SS BOND : bond 0.00378 / 0.24 ( 44) SS BOND : angle 2.88312 / 1.79 ( 88) hydrogen bonds : bond 0.09102 / 6.12 ( 540) hydrogen bonds : angle 6.32581 / 4.41 ( 1620) link_BETA1-4 : bond 0.03275 / 2.33 ( 12) link_BETA1-4 : angle 7.90904 / 3.92 ( 36) link_NAG-ASN : bond 0.01645 / 1.18 ( 28) link_NAG-ASN : angle 4.11030 / 2.74 ( 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 : 1.467 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: 0.2334 time to fit residues: 339.5201 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 : 1.506 ------------------------------------------------------------------------------- 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... A 124 ASN A 132 GLN A 217 HIS A 413 ASN 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.110806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089097 restraints weight = 118399.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092460 restraints weight = 63238.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094798 restraints weight = 40522.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096411 restraints weight = 29146.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.097540 restraints weight = 22902.574| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41504 Z= 0.184 Angle : 0.911 13.414 56478 Z= 0.445 Chirality : 0.052 0.452 6514 Planarity : 0.006 0.068 7202 Dihedral : 6.211 70.417 5516 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.59 % Favored : 90.14 % Rotamer: Outliers : 2.68 % Allowed : 14.00 % Favored : 83.31 % 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: -3.17 (0.11), residues: 5110 helix: 0.34 (0.17), residues: 860 sheet: -1.70 (0.11), residues: 1818 loop : -3.43 (0.11), residues: 2432 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 0.021 0.002 PHE D 74 TRP 0.026 0.002 TRP B1237 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (41420) covalent geometry : angle 0.89461 / 0.44 (56270) SS BOND : bond 0.00291 / 0.17 ( 44) SS BOND : angle 2.07911 / 1.40 ( 88) hydrogen bonds : bond 0.05874 / 3.96 ( 540) hydrogen bonds : angle 5.27520 / 3.64 ( 1620) link_BETA1-4 : bond 0.00655 / 0.41 ( 12) link_BETA1-4 : angle 2.85881 / 1.83 ( 36) link_NAG-ASN : bond 0.00990 / 0.70 ( 28) link_NAG-ASN : angle 3.70494 / 2.49 ( 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 : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8389 (mtp) cc_final: 0.7538 (mmm) REVERT: A 114 PHE cc_start: 0.6830 (t80) cc_final: 0.6625 (t80) REVERT: A 192 PHE cc_start: 0.7873 (t80) cc_final: 0.7652 (t80) REVERT: A 208 GLN cc_start: 0.7708 (tt0) cc_final: 0.7478 (tp-100) REVERT: A 384 ILE cc_start: 0.9466 (pt) cc_final: 0.9154 (mm) REVERT: A 387 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7964 (mtt-85) REVERT: A 415 MET cc_start: 0.6300 (ppp) cc_final: 0.5899 (ppp) REVERT: A 456 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8744 (mmmt) REVERT: A 458 PHE cc_start: 0.8163 (p90) cc_final: 0.7938 (p90) REVERT: A 672 ASP cc_start: 0.8535 (t0) cc_final: 0.8243 (t0) REVERT: A 787 ARG cc_start: 0.8459 (ptt-90) cc_final: 0.8160 (ptt-90) REVERT: A 965 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8249 (mm) REVERT: A 977 MET cc_start: 0.9274 (mmm) cc_final: 0.9063 (mmm) REVERT: A 988 ASP cc_start: 0.8956 (m-30) cc_final: 0.8578 (m-30) REVERT: A 1161 ASP cc_start: 0.8950 (p0) cc_final: 0.8647 (p0) REVERT: A 1165 GLU cc_start: 0.9122 (tt0) cc_final: 0.8845 (tt0) REVERT: A 1217 LEU cc_start: 0.9620 (mm) cc_final: 0.9287 (mp) REVERT: A 1314 MET cc_start: 0.8764 (mpp) cc_final: 0.8310 (mpp) REVERT: A 1323 TYR cc_start: 0.7222 (t80) cc_final: 0.6962 (t80) REVERT: B 31 TYR cc_start: 0.6718 (p90) cc_final: 0.6459 (p90) REVERT: B 134 ASP cc_start: 0.8120 (t0) cc_final: 0.7587 (t70) REVERT: B 183 LEU cc_start: 0.7983 (mt) cc_final: 0.7768 (mt) REVERT: B 208 GLN cc_start: 0.7929 (tt0) cc_final: 0.7676 (tp-100) REVERT: B 222 GLU cc_start: 0.8413 (pt0) cc_final: 0.8099 (pp20) REVERT: B 318 MET cc_start: 0.5348 (mmm) cc_final: 0.5122 (mmm) REVERT: B 372 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 387 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7462 (ttm-80) REVERT: B 500 MET cc_start: 0.7052 (ttt) cc_final: 0.6746 (ttt) REVERT: B 519 ASP cc_start: 0.6534 (m-30) cc_final: 0.6248 (m-30) REVERT: B 561 GLU cc_start: 0.7287 (pt0) cc_final: 0.6808 (pt0) REVERT: B 605 LEU cc_start: 0.8467 (tp) cc_final: 0.8086 (tp) REVERT: B 627 LEU cc_start: 0.9136 (tp) cc_final: 0.8907 (tt) REVERT: B 673 MET cc_start: 0.8625 (tpp) cc_final: 0.8292 (tpp) REVERT: B 688 MET cc_start: 0.8459 (ppp) cc_final: 0.8254 (ppp) REVERT: B 741 TRP cc_start: 0.8119 (t-100) cc_final: 0.7447 (t-100) REVERT: B 858 TRP cc_start: 0.7578 (m-90) cc_final: 0.7022 (m-90) REVERT: B 965 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7548 (mm) REVERT: B 977 MET cc_start: 0.9222 (mmm) cc_final: 0.8820 (mmm) REVERT: B 992 GLU cc_start: 0.8163 (tp30) cc_final: 0.7743 (tp30) REVERT: B 1161 ASP cc_start: 0.8814 (p0) cc_final: 0.8375 (p0) REVERT: B 1168 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8693 (tttm) REVERT: B 1172 GLU cc_start: 0.9001 (tt0) cc_final: 0.8277 (tm-30) REVERT: B 1323 TYR cc_start: 0.7391 (t80) cc_final: 0.7135 (t80) REVERT: C 31 TYR cc_start: 0.7275 (p90) cc_final: 0.7056 (p90) REVERT: C 114 PHE cc_start: 0.6839 (t80) cc_final: 0.6623 (t80) REVERT: C 192 PHE cc_start: 0.7888 (t80) cc_final: 0.7663 (t80) REVERT: C 373 ASP cc_start: 0.8116 (t0) cc_final: 0.7881 (t0) REVERT: C 384 ILE cc_start: 0.9471 (pt) cc_final: 0.9106 (mm) REVERT: C 415 MET cc_start: 0.6319 (ppp) cc_final: 0.5903 (ppp) REVERT: C 456 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8742 (mmmt) REVERT: C 458 PHE cc_start: 0.8230 (p90) cc_final: 0.8029 (p90) REVERT: C 672 ASP cc_start: 0.8539 (t0) cc_final: 0.8247 (t0) REVERT: C 787 ARG cc_start: 0.8442 (ptt-90) cc_final: 0.8136 (ptt-90) REVERT: C 965 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8349 (mm) REVERT: C 977 MET cc_start: 0.9272 (mmm) cc_final: 0.9051 (mmm) REVERT: C 988 ASP cc_start: 0.8971 (m-30) cc_final: 0.8639 (m-30) REVERT: C 1015 GLN cc_start: 0.8394 (tp40) cc_final: 0.7896 (tp40) REVERT: C 1109 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9065 (mm) REVERT: C 1161 ASP cc_start: 0.8941 (p0) cc_final: 0.8629 (p0) REVERT: C 1165 GLU cc_start: 0.9142 (tt0) cc_final: 0.8849 (tt0) REVERT: C 1217 LEU cc_start: 0.9613 (mm) cc_final: 0.9271 (mp) REVERT: C 1314 MET cc_start: 0.8767 (mpp) cc_final: 0.8317 (mpp) REVERT: C 1323 TYR cc_start: 0.7191 (t80) cc_final: 0.6895 (t80) REVERT: D 67 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7665 (p) REVERT: D 134 ASP cc_start: 0.8112 (t0) cc_final: 0.7608 (t70) REVERT: D 222 GLU cc_start: 0.8420 (pt0) cc_final: 0.8094 (pp20) REVERT: D 318 MET cc_start: 0.5405 (mmm) cc_final: 0.5131 (mmm) REVERT: D 372 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8301 (p) REVERT: D 387 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7721 (ttm-80) REVERT: D 500 MET cc_start: 0.6998 (ttt) cc_final: 0.6560 (ttt) REVERT: D 543 TYR cc_start: 0.7902 (p90) cc_final: 0.7659 (p90) REVERT: D 561 GLU cc_start: 0.7284 (pt0) cc_final: 0.6806 (pt0) REVERT: D 605 LEU cc_start: 0.8451 (tp) cc_final: 0.8082 (tp) REVERT: D 673 MET cc_start: 0.8630 (tpp) cc_final: 0.8218 (tpp) REVERT: D 741 TRP cc_start: 0.8139 (t-100) cc_final: 0.7448 (t-100) REVERT: D 858 TRP cc_start: 0.7577 (m-90) cc_final: 0.7002 (m-90) REVERT: D 977 MET cc_start: 0.9186 (mmm) cc_final: 0.8821 (mmm) REVERT: D 990 LEU cc_start: 0.8476 (mt) cc_final: 0.8235 (mp) REVERT: D 992 GLU cc_start: 0.8252 (tp30) cc_final: 0.7777 (tp30) REVERT: D 1018 TYR cc_start: 0.7950 (m-80) cc_final: 0.7565 (m-80) REVERT: D 1149 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9286 (tt) REVERT: D 1161 ASP cc_start: 0.8827 (p0) cc_final: 0.8400 (p0) REVERT: D 1168 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8725 (tttm) REVERT: D 1323 TYR cc_start: 0.7388 (t80) cc_final: 0.7144 (t80) outliers start: 120 outliers final: 66 residues processed: 763 average time/residue: 0.2282 time to fit residues: 297.9500 Evaluate side-chains 654 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 580 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 1109 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: 4.9990 chunk 306 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 502 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 418 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A 644 ASN A 691 GLN A 851 ASN A1020 HIS A1187 GLN A1242 GLN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 691 GLN B 961 ASN C 361 GLN C 644 ASN C 646 HIS C 691 GLN C 851 ASN C1020 HIS C1179 ASN C1187 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 691 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.103595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081527 restraints weight = 119736.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084596 restraints weight = 64396.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086820 restraints weight = 42130.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088345 restraints weight = 30699.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.089320 restraints weight = 24435.217| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 41504 Z= 0.272 Angle : 0.885 18.981 56478 Z= 0.441 Chirality : 0.051 0.380 6514 Planarity : 0.006 0.074 7202 Dihedral : 5.683 59.171 5477 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.72 % Favored : 89.04 % Rotamer: Outliers : 4.05 % Allowed : 17.27 % Favored : 78.68 % 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: -2.78 (0.11), residues: 5110 helix: 0.55 (0.17), residues: 868 sheet: -1.37 (0.12), residues: 1774 loop : -3.19 (0.11), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 370 TYR 0.030 0.002 TYR A1007 PHE 0.035 0.002 PHE B 114 TRP 0.035 0.003 TRP A 741 HIS 0.009 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.27 (41420) covalent geometry : angle 0.86932 / 0.44 (56270) SS BOND : bond 0.00417 / 0.28 ( 44) SS BOND : angle 2.49985 / 1.68 ( 88) hydrogen bonds : bond 0.05716 / 3.83 ( 540) hydrogen bonds : angle 5.56874 / 3.83 ( 1620) link_BETA1-4 : bond 0.00433 / 0.24 ( 12) link_BETA1-4 : angle 2.57322 / 1.65 ( 36) link_NAG-ASN : bond 0.00961 / 0.66 ( 28) link_NAG-ASN : angle 3.34944 / 2.24 ( 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 788 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 607 time to evaluate : 1.524 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: A 65 GLU cc_start: 0.7372 (mp0) cc_final: 0.7036 (mp0) REVERT: A 66 SER cc_start: 0.8707 (t) cc_final: 0.7896 (p) REVERT: A 216 GLU cc_start: 0.8028 (mp0) cc_final: 0.7794 (mp0) REVERT: A 224 PHE cc_start: 0.7564 (p90) cc_final: 0.7249 (p90) REVERT: A 384 ILE cc_start: 0.9566 (pt) cc_final: 0.9177 (mm) REVERT: A 415 MET cc_start: 0.6504 (ppp) cc_final: 0.6013 (ppp) REVERT: A 456 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8826 (mmmt) REVERT: A 458 PHE cc_start: 0.8473 (p90) cc_final: 0.8243 (p90) REVERT: A 567 LYS cc_start: 0.8372 (tppt) cc_final: 0.8086 (tppt) REVERT: A 672 ASP cc_start: 0.8709 (t0) cc_final: 0.8466 (t0) REVERT: A 688 MET cc_start: 0.8689 (ppp) cc_final: 0.8261 (ppp) REVERT: A 934 LYS cc_start: 0.8430 (tppt) cc_final: 0.8205 (mmmt) REVERT: A 965 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 988 ASP cc_start: 0.9092 (m-30) cc_final: 0.8765 (m-30) REVERT: A 1109 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9129 (mm) REVERT: A 1161 ASP cc_start: 0.9029 (p0) cc_final: 0.8739 (p0) REVERT: A 1165 GLU cc_start: 0.9189 (tt0) cc_final: 0.8909 (tt0) REVERT: A 1217 LEU cc_start: 0.9649 (mm) cc_final: 0.9396 (mm) REVERT: A 1242 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: A 1314 MET cc_start: 0.8767 (mpp) cc_final: 0.8081 (mpp) REVERT: B 181 PHE cc_start: 0.7629 (p90) cc_final: 0.7427 (p90) REVERT: B 208 GLN cc_start: 0.8040 (tt0) cc_final: 0.7686 (tp-100) REVERT: B 222 GLU cc_start: 0.8426 (pt0) cc_final: 0.8024 (pp20) REVERT: B 318 MET cc_start: 0.5768 (mmm) cc_final: 0.5409 (mmm) REVERT: B 373 ASP cc_start: 0.8485 (p0) cc_final: 0.7888 (t0) REVERT: B 387 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7765 (ttm-80) REVERT: B 500 MET cc_start: 0.7171 (ttt) cc_final: 0.6623 (ttt) REVERT: B 561 GLU cc_start: 0.7519 (pt0) cc_final: 0.7020 (pt0) REVERT: B 578 LEU cc_start: 0.8571 (mt) cc_final: 0.8165 (pt) REVERT: B 605 LEU cc_start: 0.8578 (tp) cc_final: 0.8264 (tp) REVERT: B 669 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 673 MET cc_start: 0.8733 (tpp) cc_final: 0.8252 (tpp) REVERT: B 741 TRP cc_start: 0.8598 (t-100) cc_final: 0.7554 (t-100) REVERT: B 782 SER cc_start: 0.8201 (t) cc_final: 0.7862 (m) REVERT: B 811 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7977 (mmtm) REVERT: B 858 TRP cc_start: 0.7626 (m-90) cc_final: 0.7059 (m-90) REVERT: B 965 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7674 (mm) REVERT: B 977 MET cc_start: 0.9313 (mmm) cc_final: 0.8832 (mmm) REVERT: B 1147 LYS cc_start: 0.9026 (mttp) cc_final: 0.8697 (mttp) REVERT: B 1161 ASP cc_start: 0.8969 (p0) cc_final: 0.8595 (p0) REVERT: B 1172 GLU cc_start: 0.9076 (tt0) cc_final: 0.8251 (tm-30) REVERT: B 1217 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9180 (mm) REVERT: B 1258 LEU cc_start: 0.8990 (mt) cc_final: 0.8640 (mp) REVERT: C 65 GLU cc_start: 0.7395 (mp0) cc_final: 0.7072 (mp0) REVERT: C 169 ASP cc_start: 0.6536 (m-30) cc_final: 0.6088 (m-30) REVERT: C 216 GLU cc_start: 0.8006 (mp0) cc_final: 0.7775 (mp0) REVERT: C 224 PHE cc_start: 0.7509 (p90) cc_final: 0.7164 (p90) REVERT: C 384 ILE cc_start: 0.9604 (pt) cc_final: 0.9184 (mm) REVERT: C 415 MET cc_start: 0.6515 (ppp) cc_final: 0.6017 (ppp) REVERT: C 456 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8750 (mmmt) REVERT: C 567 LYS cc_start: 0.8365 (tppt) cc_final: 0.8081 (tppt) REVERT: C 672 ASP cc_start: 0.8708 (t0) cc_final: 0.8454 (t0) REVERT: C 688 MET cc_start: 0.8679 (ppp) cc_final: 0.8246 (ppp) REVERT: C 934 LYS cc_start: 0.8431 (tppt) cc_final: 0.8228 (mmmt) REVERT: C 965 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 977 MET cc_start: 0.9319 (mmm) cc_final: 0.9088 (mmm) REVERT: C 988 ASP cc_start: 0.9094 (m-30) cc_final: 0.8759 (m-30) REVERT: C 1015 GLN cc_start: 0.8298 (tp40) cc_final: 0.7944 (tp40) REVERT: C 1109 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9098 (mm) REVERT: C 1161 ASP cc_start: 0.9019 (p0) cc_final: 0.8725 (p0) REVERT: C 1165 GLU cc_start: 0.9213 (tt0) cc_final: 0.8918 (tt0) REVERT: C 1217 LEU cc_start: 0.9646 (mm) cc_final: 0.9379 (mm) REVERT: C 1314 MET cc_start: 0.8778 (mpp) cc_final: 0.8098 (mpp) REVERT: D 181 PHE cc_start: 0.7724 (p90) cc_final: 0.7513 (p90) REVERT: D 222 GLU cc_start: 0.8410 (pt0) cc_final: 0.8022 (pp20) REVERT: D 318 MET cc_start: 0.5807 (mmm) cc_final: 0.5437 (mmm) REVERT: D 373 ASP cc_start: 0.8535 (p0) cc_final: 0.7988 (t0) REVERT: D 387 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7762 (ttm-80) REVERT: D 500 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6607 (ttt) REVERT: D 519 ASP cc_start: 0.6634 (m-30) cc_final: 0.6387 (m-30) REVERT: D 541 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6060 (pt) REVERT: D 543 TYR cc_start: 0.8193 (p90) cc_final: 0.7583 (p90) REVERT: D 561 GLU cc_start: 0.7395 (pt0) cc_final: 0.6879 (pt0) REVERT: D 578 LEU cc_start: 0.8566 (mt) cc_final: 0.8156 (pt) REVERT: D 605 LEU cc_start: 0.8604 (tp) cc_final: 0.8287 (tp) REVERT: D 669 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8578 (t80) REVERT: D 673 MET cc_start: 0.8832 (tpp) cc_final: 0.8276 (tpp) REVERT: D 741 TRP cc_start: 0.8600 (t-100) cc_final: 0.7619 (t-100) REVERT: D 782 SER cc_start: 0.8177 (t) cc_final: 0.7846 (m) REVERT: D 786 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7329 (mp) REVERT: D 858 TRP cc_start: 0.7652 (m-90) cc_final: 0.7062 (m-90) REVERT: D 977 MET cc_start: 0.9386 (mmm) cc_final: 0.8995 (mmm) REVERT: D 990 LEU cc_start: 0.8704 (mt) cc_final: 0.8442 (mp) REVERT: D 1018 TYR cc_start: 0.8100 (m-80) cc_final: 0.7566 (m-80) REVERT: D 1147 LYS cc_start: 0.8995 (mttp) cc_final: 0.8685 (mttp) REVERT: D 1149 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9360 (tt) REVERT: D 1161 ASP cc_start: 0.8981 (p0) cc_final: 0.8623 (p0) REVERT: D 1217 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9175 (mm) REVERT: D 1258 LEU cc_start: 0.8995 (mt) cc_final: 0.8664 (mp) outliers start: 181 outliers final: 82 residues processed: 738 average time/residue: 0.2164 time to fit residues: 276.2260 Evaluate side-chains 646 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 550 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 355 VAL 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 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 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain B residue 48 CYS 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 384 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 645 ARG 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 1110 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 50 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 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 486 THR Chi-restraints excluded: chain C residue 523 HIS 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 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 1206 VAL Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 183 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 348 THR Chi-restraints excluded: chain D residue 476 VAL 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 550 ASP Chi-restraints excluded: chain D residue 645 ARG 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 1101 LEU Chi-restraints excluded: chain D residue 1110 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 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 341 optimal weight: 0.0970 chunk 169 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 406 optimal weight: 7.9990 chunk 392 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 381 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 chunk 385 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A 983 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 GLN ** B1241 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 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN C 983 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 132 GLN D 182 GLN ** D 441 HIS ** 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 = 0.3909 r_free = 0.3909 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.083753 restraints weight = 117405.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.086910 restraints weight = 62946.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089188 restraints weight = 40957.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090761 restraints weight = 29715.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091809 restraints weight = 23597.490| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41504 Z= 0.164 Angle : 0.805 14.509 56478 Z= 0.390 Chirality : 0.049 0.349 6514 Planarity : 0.005 0.071 7202 Dihedral : 5.512 60.763 5473 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.00 % Favored : 90.74 % Rotamer: Outliers : 3.83 % Allowed : 19.28 % Favored : 76.89 % 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: -2.50 (0.11), residues: 5110 helix: 0.89 (0.18), residues: 856 sheet: -1.23 (0.12), residues: 1740 loop : -2.99 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 539 TYR 0.029 0.002 TYR B1007 PHE 0.021 0.002 PHE B 808 TRP 0.014 0.002 TRP D1132 HIS 0.008 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (41420) covalent geometry : angle 0.79161 / 0.39 (56270) SS BOND : bond 0.00263 / 0.15 ( 44) SS BOND : angle 1.83731 / 1.23 ( 88) hydrogen bonds : bond 0.05210 / 3.52 ( 540) hydrogen bonds : angle 5.22041 / 3.60 ( 1620) link_BETA1-4 : bond 0.00465 / 0.26 ( 12) link_BETA1-4 : angle 2.38800 / 1.58 ( 36) link_NAG-ASN : bond 0.00801 / 0.55 ( 28) link_NAG-ASN : angle 3.23576 / 2.18 ( 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 780 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 609 time to evaluate : 1.457 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 65 GLU cc_start: 0.7396 (mp0) cc_final: 0.7189 (mp0) REVERT: A 66 SER cc_start: 0.8646 (t) cc_final: 0.7866 (p) REVERT: A 216 GLU cc_start: 0.8107 (mp0) cc_final: 0.7898 (mp0) REVERT: A 224 PHE cc_start: 0.7625 (p90) cc_final: 0.7425 (p90) REVERT: A 309 PHE cc_start: 0.8668 (m-80) cc_final: 0.8366 (m-80) REVERT: A 384 ILE cc_start: 0.9540 (pt) cc_final: 0.9173 (mm) REVERT: A 456 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8827 (mmmm) REVERT: A 567 LYS cc_start: 0.8339 (tppt) cc_final: 0.8061 (tppt) REVERT: A 672 ASP cc_start: 0.8617 (t0) cc_final: 0.8337 (t0) REVERT: A 688 MET cc_start: 0.8738 (ppp) cc_final: 0.8363 (ppp) REVERT: A 965 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8150 (mm) REVERT: A 988 ASP cc_start: 0.8969 (m-30) cc_final: 0.8612 (m-30) REVERT: A 1109 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9053 (mm) REVERT: A 1149 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9367 (tt) REVERT: A 1161 ASP cc_start: 0.8946 (p0) cc_final: 0.8631 (p0) REVERT: A 1165 GLU cc_start: 0.9153 (tt0) cc_final: 0.8864 (tt0) REVERT: A 1217 LEU cc_start: 0.9630 (mm) cc_final: 0.9421 (mt) REVERT: A 1314 MET cc_start: 0.8792 (mpp) cc_final: 0.8130 (mpp) REVERT: B 181 PHE cc_start: 0.7647 (p90) cc_final: 0.7409 (p90) REVERT: B 208 GLN cc_start: 0.7979 (tt0) cc_final: 0.7678 (tp-100) REVERT: B 222 GLU cc_start: 0.8409 (pt0) cc_final: 0.8087 (pp20) REVERT: B 318 MET cc_start: 0.5692 (mmm) cc_final: 0.5230 (tpt) REVERT: B 373 ASP cc_start: 0.8331 (p0) cc_final: 0.7824 (t0) REVERT: B 387 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7564 (ttm-80) REVERT: B 500 MET cc_start: 0.6893 (ttt) cc_final: 0.6607 (ttt) REVERT: B 561 GLU cc_start: 0.7405 (pt0) cc_final: 0.6960 (pt0) REVERT: B 578 LEU cc_start: 0.8550 (mt) cc_final: 0.7948 (pp) REVERT: B 605 LEU cc_start: 0.8537 (tp) cc_final: 0.8205 (tp) REVERT: B 656 THR cc_start: -0.2087 (OUTLIER) cc_final: -0.2304 (t) REVERT: B 673 MET cc_start: 0.8584 (tpp) cc_final: 0.8094 (tpp) REVERT: B 782 SER cc_start: 0.8067 (t) cc_final: 0.7837 (m) REVERT: B 786 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7109 (tt) REVERT: B 811 LYS cc_start: 0.8184 (mmtp) cc_final: 0.7853 (mmtm) REVERT: B 858 TRP cc_start: 0.7588 (m-90) cc_final: 0.7042 (m-90) REVERT: B 965 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7764 (mm) REVERT: B 977 MET cc_start: 0.9231 (mmm) cc_final: 0.8754 (mmm) REVERT: B 1018 TYR cc_start: 0.8031 (m-80) cc_final: 0.7614 (m-80) REVERT: B 1147 LYS cc_start: 0.9043 (mttp) cc_final: 0.8679 (mttp) REVERT: B 1161 ASP cc_start: 0.8957 (p0) cc_final: 0.8583 (p0) REVERT: B 1172 GLU cc_start: 0.9044 (tt0) cc_final: 0.8233 (tm-30) REVERT: B 1217 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9145 (mm) REVERT: C 31 TYR cc_start: 0.6823 (p90) cc_final: 0.6532 (p90) REVERT: C 65 GLU cc_start: 0.7408 (mp0) cc_final: 0.7203 (mp0) REVERT: C 66 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.7943 (p) REVERT: C 216 GLU cc_start: 0.8088 (mp0) cc_final: 0.7886 (mp0) REVERT: C 224 PHE cc_start: 0.7577 (p90) cc_final: 0.7346 (p90) REVERT: C 309 PHE cc_start: 0.8627 (m-80) cc_final: 0.8321 (m-80) REVERT: C 318 MET cc_start: 0.5701 (ttm) cc_final: 0.5439 (tpt) REVERT: C 384 ILE cc_start: 0.9582 (pt) cc_final: 0.9127 (mm) REVERT: C 456 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8841 (mmmm) REVERT: C 567 LYS cc_start: 0.8336 (tppt) cc_final: 0.8086 (tppt) REVERT: C 672 ASP cc_start: 0.8614 (t0) cc_final: 0.8335 (t0) REVERT: C 688 MET cc_start: 0.8768 (ppp) cc_final: 0.8406 (ppp) REVERT: C 965 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8148 (mm) REVERT: C 977 MET cc_start: 0.9301 (mmm) cc_final: 0.8990 (mmm) REVERT: C 988 ASP cc_start: 0.8971 (m-30) cc_final: 0.8628 (m-30) REVERT: C 1015 GLN cc_start: 0.8375 (tp40) cc_final: 0.7860 (tp40) REVERT: C 1018 TYR cc_start: 0.8188 (m-80) cc_final: 0.7929 (m-80) REVERT: C 1149 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9421 (tt) REVERT: C 1161 ASP cc_start: 0.8947 (p0) cc_final: 0.8629 (p0) REVERT: C 1165 GLU cc_start: 0.9176 (tt0) cc_final: 0.8881 (tt0) REVERT: C 1217 LEU cc_start: 0.9641 (mm) cc_final: 0.9412 (mm) REVERT: C 1314 MET cc_start: 0.8797 (mpp) cc_final: 0.8136 (mpp) REVERT: D 74 PHE cc_start: 0.8426 (t80) cc_final: 0.8182 (t80) REVERT: D 181 PHE cc_start: 0.7742 (p90) cc_final: 0.7540 (p90) REVERT: D 222 GLU cc_start: 0.8404 (pt0) cc_final: 0.8083 (pp20) REVERT: D 318 MET cc_start: 0.5681 (mmm) cc_final: 0.5344 (mmm) REVERT: D 373 ASP cc_start: 0.8365 (p0) cc_final: 0.7886 (t0) REVERT: D 387 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7548 (ttm-80) REVERT: D 500 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6510 (ttt) REVERT: D 541 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6252 (pt) REVERT: D 561 GLU cc_start: 0.7407 (pt0) cc_final: 0.6958 (pt0) REVERT: D 578 LEU cc_start: 0.8517 (mt) cc_final: 0.7891 (pp) REVERT: D 605 LEU cc_start: 0.8547 (tp) cc_final: 0.8198 (tp) REVERT: D 672 ASP cc_start: 0.8869 (t0) cc_final: 0.8651 (t0) REVERT: D 673 MET cc_start: 0.8626 (tpp) cc_final: 0.8179 (tpp) REVERT: D 782 SER cc_start: 0.8052 (t) cc_final: 0.7825 (m) REVERT: D 858 TRP cc_start: 0.7518 (m-90) cc_final: 0.7023 (m-90) REVERT: D 977 MET cc_start: 0.9265 (mmm) cc_final: 0.8718 (mmm) REVERT: D 1018 TYR cc_start: 0.8045 (m-80) cc_final: 0.7615 (m-80) REVERT: D 1147 LYS cc_start: 0.8996 (mttp) cc_final: 0.8505 (mttp) REVERT: D 1149 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9344 (tt) REVERT: D 1161 ASP cc_start: 0.8963 (p0) cc_final: 0.8614 (p0) REVERT: D 1217 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9151 (mm) outliers start: 171 outliers final: 86 residues processed: 734 average time/residue: 0.2055 time to fit residues: 261.0229 Evaluate side-chains 653 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 553 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 VAL 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 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 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 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 1270 THR Chi-restraints excluded: chain B residue 253 LEU 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 645 ARG 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 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1080 PHE 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 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 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 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 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 965 LEU Chi-restraints excluded: chain C residue 1055 TYR 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 286 PHE Chi-restraints excluded: chain D residue 348 THR 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 654 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU 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 1251 THR 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: 9.9990 chunk 417 optimal weight: 7.9990 chunk 409 optimal weight: 9.9990 chunk 451 optimal weight: 8.9990 chunk 264 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 397 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 456 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 466 HIS A 851 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1241 GLN B1242 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS C 851 ASN C1242 GLN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.105665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.083599 restraints weight = 116354.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086820 restraints weight = 62134.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.089036 restraints weight = 40106.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090588 restraints weight = 29103.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.091584 restraints weight = 23103.182| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 41504 Z= 0.160 Angle : 0.801 15.210 56478 Z= 0.385 Chirality : 0.049 0.348 6514 Planarity : 0.005 0.060 7202 Dihedral : 5.292 36.083 5470 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.82 % Favored : 89.98 % Rotamer: Outliers : 3.78 % Allowed : 20.65 % Favored : 75.57 % 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: -2.30 (0.11), residues: 5110 helix: 0.91 (0.18), residues: 860 sheet: -1.02 (0.12), residues: 1712 loop : -2.86 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 507 TYR 0.036 0.002 TYR D1007 PHE 0.025 0.002 PHE C 114 TRP 0.015 0.001 TRP A 436 HIS 0.008 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (41420) covalent geometry : angle 0.78713 / 0.38 (56270) SS BOND : bond 0.00297 / 0.21 ( 44) SS BOND : angle 2.01579 / 1.40 ( 88) hydrogen bonds : bond 0.04972 / 3.33 ( 540) hydrogen bonds : angle 5.18876 / 3.58 ( 1620) link_BETA1-4 : bond 0.00505 / 0.31 ( 12) link_BETA1-4 : angle 2.38269 / 1.58 ( 36) link_NAG-ASN : bond 0.00782 / 0.54 ( 28) link_NAG-ASN : angle 3.13772 / 2.11 ( 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 758 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 589 time to evaluate : 1.658 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: A 65 GLU cc_start: 0.7462 (mp0) cc_final: 0.7253 (mp0) REVERT: A 66 SER cc_start: 0.8736 (t) cc_final: 0.8054 (p) REVERT: A 310 GLN cc_start: 0.8589 (mp10) cc_final: 0.8350 (pm20) REVERT: A 384 ILE cc_start: 0.9548 (pt) cc_final: 0.9176 (mm) REVERT: A 456 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8721 (mmmm) REVERT: A 543 TYR cc_start: 0.7565 (p90) cc_final: 0.7253 (p90) REVERT: A 567 LYS cc_start: 0.8336 (tppt) cc_final: 0.8084 (tppt) REVERT: A 672 ASP cc_start: 0.8650 (t0) cc_final: 0.8380 (t0) REVERT: A 673 MET cc_start: 0.8911 (tpp) cc_final: 0.8705 (tpp) REVERT: A 965 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8261 (mm) REVERT: A 988 ASP cc_start: 0.8982 (m-30) cc_final: 0.8619 (m-30) REVERT: A 1109 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 1149 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9379 (tt) REVERT: A 1161 ASP cc_start: 0.8951 (p0) cc_final: 0.8638 (p0) REVERT: A 1165 GLU cc_start: 0.9166 (tt0) cc_final: 0.8878 (tt0) REVERT: A 1217 LEU cc_start: 0.9610 (mm) cc_final: 0.9402 (mm) REVERT: A 1314 MET cc_start: 0.8786 (mpp) cc_final: 0.8085 (mpp) REVERT: B 181 PHE cc_start: 0.7710 (p90) cc_final: 0.7471 (p90) REVERT: B 208 GLN cc_start: 0.7912 (tt0) cc_final: 0.7684 (tp-100) REVERT: B 222 GLU cc_start: 0.8372 (pt0) cc_final: 0.8073 (pp20) REVERT: B 318 MET cc_start: 0.5655 (mmm) cc_final: 0.5196 (tpt) REVERT: B 373 ASP cc_start: 0.8337 (p0) cc_final: 0.7913 (t0) REVERT: B 387 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7506 (ttm-80) REVERT: B 500 MET cc_start: 0.6977 (ttt) cc_final: 0.6672 (ttt) REVERT: B 520 MET cc_start: 0.7531 (tmm) cc_final: 0.7168 (tmm) REVERT: B 561 GLU cc_start: 0.7510 (pt0) cc_final: 0.7070 (pt0) REVERT: B 578 LEU cc_start: 0.8426 (mt) cc_final: 0.7882 (pp) REVERT: B 605 LEU cc_start: 0.8505 (tp) cc_final: 0.8167 (tp) REVERT: B 656 THR cc_start: -0.2080 (OUTLIER) cc_final: -0.2306 (t) REVERT: B 673 MET cc_start: 0.8611 (tpp) cc_final: 0.8027 (tpp) REVERT: B 688 MET cc_start: 0.8273 (ppp) cc_final: 0.7816 (ppp) REVERT: B 741 TRP cc_start: 0.8572 (t-100) cc_final: 0.8213 (t-100) REVERT: B 782 SER cc_start: 0.8085 (t) cc_final: 0.7848 (m) REVERT: B 786 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7137 (tt) REVERT: B 811 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7855 (mmtm) REVERT: B 858 TRP cc_start: 0.7614 (m-90) cc_final: 0.7045 (m-90) REVERT: B 965 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7845 (mm) REVERT: B 977 MET cc_start: 0.9227 (mmm) cc_final: 0.8761 (mmm) REVERT: B 1018 TYR cc_start: 0.8041 (m-80) cc_final: 0.7665 (m-80) REVERT: B 1147 LYS cc_start: 0.9037 (mttp) cc_final: 0.8571 (mttp) REVERT: B 1161 ASP cc_start: 0.8978 (p0) cc_final: 0.8630 (p0) REVERT: B 1172 GLU cc_start: 0.9049 (tt0) cc_final: 0.8208 (tm-30) REVERT: B 1217 LEU cc_start: 0.9378 (mm) cc_final: 0.9144 (mm) REVERT: C 65 GLU cc_start: 0.7475 (mp0) cc_final: 0.7257 (mp0) REVERT: C 66 SER cc_start: 0.8705 (t) cc_final: 0.8034 (p) REVERT: C 216 GLU cc_start: 0.8094 (mp0) cc_final: 0.7875 (mp0) REVERT: C 384 ILE cc_start: 0.9589 (pt) cc_final: 0.9116 (mm) REVERT: C 456 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8619 (mmmm) REVERT: C 543 TYR cc_start: 0.7550 (p90) cc_final: 0.6961 (p90) REVERT: C 567 LYS cc_start: 0.8328 (tppt) cc_final: 0.8071 (tppt) REVERT: C 672 ASP cc_start: 0.8645 (t0) cc_final: 0.8349 (t0) REVERT: C 673 MET cc_start: 0.9017 (tpp) cc_final: 0.8776 (tpp) REVERT: C 965 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 977 MET cc_start: 0.9279 (mmm) cc_final: 0.8854 (mmm) REVERT: C 988 ASP cc_start: 0.8870 (m-30) cc_final: 0.8577 (m-30) REVERT: C 1015 GLN cc_start: 0.8425 (tp40) cc_final: 0.7867 (tp40) REVERT: C 1016 LEU cc_start: 0.8996 (mp) cc_final: 0.8786 (mp) REVERT: C 1018 TYR cc_start: 0.8209 (m-80) cc_final: 0.7969 (m-80) REVERT: C 1074 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8389 (tp-100) REVERT: C 1109 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9065 (mm) REVERT: C 1149 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9365 (tt) REVERT: C 1161 ASP cc_start: 0.8963 (p0) cc_final: 0.8635 (p0) REVERT: C 1165 GLU cc_start: 0.9173 (tt0) cc_final: 0.8875 (tt0) REVERT: C 1217 LEU cc_start: 0.9628 (mm) cc_final: 0.9388 (mm) REVERT: C 1242 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8008 (tp40) REVERT: C 1314 MET cc_start: 0.8818 (mpp) cc_final: 0.8142 (mpp) REVERT: D 74 PHE cc_start: 0.8458 (t80) cc_final: 0.8175 (t80) REVERT: D 222 GLU cc_start: 0.8361 (pt0) cc_final: 0.8022 (pp20) REVERT: D 246 MET cc_start: 0.7934 (mtm) cc_final: 0.7732 (mtp) REVERT: D 318 MET cc_start: 0.5682 (mmm) cc_final: 0.5243 (tpt) REVERT: D 373 ASP cc_start: 0.8330 (p0) cc_final: 0.7916 (t0) REVERT: D 387 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7592 (ttm-80) REVERT: D 500 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6516 (ttt) REVERT: D 520 MET cc_start: 0.7496 (tmm) cc_final: 0.7213 (tmm) REVERT: D 541 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6267 (pt) REVERT: D 561 GLU cc_start: 0.7506 (pt0) cc_final: 0.7075 (pt0) REVERT: D 578 LEU cc_start: 0.8434 (mt) cc_final: 0.7893 (pp) REVERT: D 605 LEU cc_start: 0.8521 (tp) cc_final: 0.8150 (tp) REVERT: D 672 ASP cc_start: 0.8813 (t0) cc_final: 0.8543 (t0) REVERT: D 673 MET cc_start: 0.8580 (tpp) cc_final: 0.8107 (tpp) REVERT: D 688 MET cc_start: 0.8325 (ppp) cc_final: 0.7972 (ppp) REVERT: D 741 TRP cc_start: 0.8591 (t-100) cc_final: 0.8252 (t-100) REVERT: D 782 SER cc_start: 0.8058 (t) cc_final: 0.7830 (m) REVERT: D 786 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7119 (tt) REVERT: D 858 TRP cc_start: 0.7574 (m-90) cc_final: 0.7054 (m-90) REVERT: D 977 MET cc_start: 0.9278 (mmm) cc_final: 0.8891 (mmm) REVERT: D 1018 TYR cc_start: 0.8048 (m-80) cc_final: 0.7686 (m-10) REVERT: D 1035 ASN cc_start: 0.7953 (m-40) cc_final: 0.7633 (m110) REVERT: D 1147 LYS cc_start: 0.8973 (mttp) cc_final: 0.8616 (mttp) REVERT: D 1149 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9340 (tt) REVERT: D 1161 ASP cc_start: 0.8978 (p0) cc_final: 0.8627 (p0) REVERT: D 1217 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9145 (mm) outliers start: 169 outliers final: 109 residues processed: 710 average time/residue: 0.2056 time to fit residues: 253.1212 Evaluate side-chains 675 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 550 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 VAL 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 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 514 LEU 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 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 965 LEU 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 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS 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 384 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG 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 761 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1110 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 1299 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 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 564 LEU Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 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 949 SER Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1074 GLN 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 1242 GLN 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 348 THR Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR 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 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 1101 LEU Chi-restraints excluded: chain D residue 1110 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 1305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 49 optimal weight: 5.9990 chunk 445 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 384 optimal weight: 0.0000 chunk 75 optimal weight: 10.0000 chunk 289 optimal weight: 0.8980 chunk 419 optimal weight: 10.0000 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1179 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN C1179 ASN C1252 GLN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.104015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081788 restraints weight = 117641.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.084962 restraints weight = 62910.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.087154 restraints weight = 40665.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088664 restraints weight = 29570.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.089662 restraints weight = 23596.286| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 41504 Z= 0.197 Angle : 0.801 14.223 56478 Z= 0.387 Chirality : 0.049 0.467 6514 Planarity : 0.005 0.058 7202 Dihedral : 5.349 31.137 5470 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.06 % Favored : 89.78 % Rotamer: Outliers : 3.96 % Allowed : 21.72 % Favored : 74.32 % 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: -2.27 (0.11), residues: 5110 helix: 0.85 (0.18), residues: 858 sheet: -0.96 (0.12), residues: 1724 loop : -2.84 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 360 TYR 0.039 0.002 TYR D1007 PHE 0.031 0.002 PHE C 224 TRP 0.015 0.002 TRP C 436 HIS 0.007 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (41420) covalent geometry : angle 0.78681 / 0.38 (56270) SS BOND : bond 0.00369 / 0.25 ( 44) SS BOND : angle 1.93079 / 1.30 ( 88) hydrogen bonds : bond 0.05026 / 3.38 ( 540) hydrogen bonds : angle 5.17649 / 3.55 ( 1620) link_BETA1-4 : bond 0.00415 / 0.26 ( 12) link_BETA1-4 : angle 2.41811 / 1.60 ( 36) link_NAG-ASN : bond 0.00878 / 0.63 ( 28) link_NAG-ASN : angle 3.12790 / 2.10 ( 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 749 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 572 time to evaluate : 1.557 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 66 SER cc_start: 0.8903 (t) cc_final: 0.8412 (p) REVERT: A 216 GLU cc_start: 0.8148 (mp0) cc_final: 0.7930 (mp0) REVERT: A 310 GLN cc_start: 0.8578 (mp10) cc_final: 0.8337 (pm20) REVERT: A 384 ILE cc_start: 0.9558 (pt) cc_final: 0.9189 (mm) REVERT: A 456 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8780 (mmmm) REVERT: A 567 LYS cc_start: 0.8357 (tppt) cc_final: 0.8103 (tppt) REVERT: A 672 ASP cc_start: 0.8649 (t0) cc_final: 0.8377 (t0) REVERT: A 965 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 988 ASP cc_start: 0.8993 (m-30) cc_final: 0.8635 (m-30) REVERT: A 1109 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9072 (mm) REVERT: A 1149 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9402 (tt) REVERT: A 1161 ASP cc_start: 0.8956 (p0) cc_final: 0.8645 (p0) REVERT: A 1165 GLU cc_start: 0.9187 (tt0) cc_final: 0.8889 (tt0) REVERT: A 1314 MET cc_start: 0.8778 (mpp) cc_final: 0.8040 (mpp) REVERT: B 208 GLN cc_start: 0.7945 (tt0) cc_final: 0.7713 (tp-100) REVERT: B 222 GLU cc_start: 0.8340 (pt0) cc_final: 0.8008 (pp20) REVERT: B 246 MET cc_start: 0.8161 (mtp) cc_final: 0.7958 (mmm) REVERT: B 318 MET cc_start: 0.5592 (mmm) cc_final: 0.5222 (tpt) REVERT: B 373 ASP cc_start: 0.8372 (p0) cc_final: 0.7988 (t0) REVERT: B 387 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7785 (ttm-80) REVERT: B 500 MET cc_start: 0.7150 (ttt) cc_final: 0.6833 (ttt) REVERT: B 520 MET cc_start: 0.7519 (tmm) cc_final: 0.7172 (tmm) REVERT: B 561 GLU cc_start: 0.7475 (pt0) cc_final: 0.7030 (pt0) REVERT: B 578 LEU cc_start: 0.8519 (mt) cc_final: 0.7942 (pp) REVERT: B 605 LEU cc_start: 0.8514 (tp) cc_final: 0.8198 (tp) REVERT: B 669 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8627 (t80) REVERT: B 672 ASP cc_start: 0.8837 (t0) cc_final: 0.8580 (t0) REVERT: B 673 MET cc_start: 0.8640 (tpp) cc_final: 0.8052 (tpp) REVERT: B 688 MET cc_start: 0.8371 (ppp) cc_final: 0.8006 (ppp) REVERT: B 782 SER cc_start: 0.8066 (t) cc_final: 0.7854 (m) REVERT: B 858 TRP cc_start: 0.7661 (m-90) cc_final: 0.7110 (m-90) REVERT: B 977 MET cc_start: 0.9217 (mmm) cc_final: 0.8681 (mmm) REVERT: B 1018 TYR cc_start: 0.8014 (m-80) cc_final: 0.7730 (m-80) REVERT: B 1147 LYS cc_start: 0.9090 (mttp) cc_final: 0.8594 (mttp) REVERT: B 1161 ASP cc_start: 0.8996 (p0) cc_final: 0.8674 (p0) REVERT: B 1172 GLU cc_start: 0.9070 (tt0) cc_final: 0.8214 (tm-30) REVERT: B 1217 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9194 (mm) REVERT: C 65 GLU cc_start: 0.7603 (mp0) cc_final: 0.7280 (mp0) REVERT: C 66 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 199 PHE cc_start: 0.8010 (m-80) cc_final: 0.7786 (m-80) REVERT: C 216 GLU cc_start: 0.8090 (mp0) cc_final: 0.7862 (mp0) REVERT: C 318 MET cc_start: 0.5370 (tpt) cc_final: 0.4978 (tpt) REVERT: C 384 ILE cc_start: 0.9582 (pt) cc_final: 0.9100 (mm) REVERT: C 456 LYS cc_start: 0.9162 (mmmt) cc_final: 0.8751 (mmmm) REVERT: C 543 TYR cc_start: 0.7554 (p90) cc_final: 0.7256 (p90) REVERT: C 567 LYS cc_start: 0.8370 (tppt) cc_final: 0.8116 (tppt) REVERT: C 672 ASP cc_start: 0.8651 (t0) cc_final: 0.8372 (t0) REVERT: C 965 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 968 MET cc_start: 0.8233 (tpt) cc_final: 0.6956 (pmm) REVERT: C 977 MET cc_start: 0.9264 (mmm) cc_final: 0.8865 (mmm) REVERT: C 988 ASP cc_start: 0.8910 (m-30) cc_final: 0.8601 (m-30) REVERT: C 1015 GLN cc_start: 0.8448 (tp40) cc_final: 0.7986 (tp40) REVERT: C 1016 LEU cc_start: 0.9007 (mp) cc_final: 0.8798 (mp) REVERT: C 1018 TYR cc_start: 0.8269 (m-80) cc_final: 0.8031 (m-80) REVERT: C 1109 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9063 (mm) REVERT: C 1149 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9337 (tp) REVERT: C 1161 ASP cc_start: 0.8969 (p0) cc_final: 0.8663 (p0) REVERT: C 1165 GLU cc_start: 0.9160 (tt0) cc_final: 0.8863 (tt0) REVERT: C 1217 LEU cc_start: 0.9633 (mm) cc_final: 0.9396 (mm) REVERT: C 1242 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: C 1314 MET cc_start: 0.8816 (mpp) cc_final: 0.8092 (mpp) REVERT: D 74 PHE cc_start: 0.8473 (t80) cc_final: 0.8176 (t80) REVERT: D 183 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7245 (mp) REVERT: D 222 GLU cc_start: 0.8319 (pt0) cc_final: 0.8005 (pp20) REVERT: D 318 MET cc_start: 0.5571 (mmm) cc_final: 0.5205 (tpt) REVERT: D 356 ASP cc_start: 0.8800 (m-30) cc_final: 0.8510 (m-30) REVERT: D 373 ASP cc_start: 0.8364 (p0) cc_final: 0.7992 (t0) REVERT: D 387 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7813 (ttm-80) REVERT: D 500 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6626 (ttt) REVERT: D 520 MET cc_start: 0.7472 (tmm) cc_final: 0.7196 (tmm) REVERT: D 541 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6208 (pt) REVERT: D 561 GLU cc_start: 0.7464 (pt0) cc_final: 0.7019 (pt0) REVERT: D 578 LEU cc_start: 0.8522 (mt) cc_final: 0.7948 (pp) REVERT: D 605 LEU cc_start: 0.8551 (tp) cc_final: 0.8229 (tp) REVERT: D 672 ASP cc_start: 0.8861 (t0) cc_final: 0.8562 (t0) REVERT: D 673 MET cc_start: 0.8654 (tpp) cc_final: 0.8145 (tpp) REVERT: D 688 MET cc_start: 0.8397 (ppp) cc_final: 0.8017 (ppp) REVERT: D 782 SER cc_start: 0.8059 (t) cc_final: 0.7855 (m) REVERT: D 965 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7208 (mm) REVERT: D 1018 TYR cc_start: 0.8019 (m-80) cc_final: 0.7637 (m-80) REVERT: D 1035 ASN cc_start: 0.7963 (m-40) cc_final: 0.7578 (m110) REVERT: D 1147 LYS cc_start: 0.9086 (mttp) cc_final: 0.8641 (mttp) REVERT: D 1149 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9366 (tt) REVERT: D 1161 ASP cc_start: 0.8983 (p0) cc_final: 0.8675 (p0) REVERT: D 1217 LEU cc_start: 0.9402 (mm) cc_final: 0.9192 (mm) outliers start: 177 outliers final: 126 residues processed: 696 average time/residue: 0.2062 time to fit residues: 250.1333 Evaluate side-chains 687 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 546 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 VAL 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 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 514 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 546 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 965 LEU 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 1251 THR Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 253 LEU 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 355 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 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 761 THR 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 1110 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 1299 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 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 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 546 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 798 MET 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 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 1206 VAL Chi-restraints excluded: chain C residue 1242 GLN Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 183 LEU 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 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR 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 1110 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 503 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 448 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 422 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 266 optimal weight: 0.7980 chunk 353 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 ASN B1242 GLN C 30 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.108635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.087166 restraints weight = 115942.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090252 restraints weight = 61660.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.092445 restraints weight = 39989.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.093921 restraints weight = 29112.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.094983 restraints weight = 23203.144| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41504 Z= 0.132 Angle : 0.779 13.824 56478 Z= 0.370 Chirality : 0.048 0.377 6514 Planarity : 0.005 0.057 7202 Dihedral : 5.104 29.245 5470 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 3.40 % Allowed : 22.66 % Favored : 73.94 % 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: -2.09 (0.12), residues: 5110 helix: 0.87 (0.17), residues: 876 sheet: -0.82 (0.12), residues: 1758 loop : -2.75 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 507 TYR 0.031 0.002 TYR D1007 PHE 0.034 0.002 PHE D 181 TRP 0.016 0.001 TRP A 436 HIS 0.006 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (41420) covalent geometry : angle 0.76693 / 0.37 (56270) SS BOND : bond 0.00282 / 0.21 ( 44) SS BOND : angle 1.59273 / 1.03 ( 88) hydrogen bonds : bond 0.04699 / 3.14 ( 540) hydrogen bonds : angle 4.92816 / 3.38 ( 1620) link_BETA1-4 : bond 0.00497 / 0.30 ( 12) link_BETA1-4 : angle 2.37967 / 1.61 ( 36) link_NAG-ASN : bond 0.00716 / 0.50 ( 28) link_NAG-ASN : angle 3.03626 / 2.04 ( 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 776 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 624 time to evaluate : 1.524 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: A 66 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 199 PHE cc_start: 0.7959 (m-80) cc_final: 0.7731 (m-80) REVERT: A 310 GLN cc_start: 0.8427 (mp10) cc_final: 0.8181 (pm20) REVERT: A 384 ILE cc_start: 0.9480 (pt) cc_final: 0.9266 (mp) REVERT: A 456 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8694 (mmmm) REVERT: A 543 TYR cc_start: 0.7270 (p90) cc_final: 0.6805 (p90) REVERT: A 567 LYS cc_start: 0.8315 (tppt) cc_final: 0.8068 (tppt) REVERT: A 582 HIS cc_start: 0.7084 (t70) cc_final: 0.6802 (t70) REVERT: A 612 GLU cc_start: 0.6665 (pm20) cc_final: 0.6452 (pm20) REVERT: A 988 ASP cc_start: 0.8913 (m-30) cc_final: 0.8499 (m-30) REVERT: A 1016 LEU cc_start: 0.9120 (mp) cc_final: 0.8901 (mp) REVERT: A 1109 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9011 (mm) REVERT: A 1149 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9364 (tt) REVERT: A 1161 ASP cc_start: 0.8896 (p0) cc_final: 0.8583 (p0) REVERT: A 1165 GLU cc_start: 0.9133 (tt0) cc_final: 0.8831 (tt0) REVERT: A 1314 MET cc_start: 0.8795 (mpp) cc_final: 0.8159 (mpp) REVERT: B 114 PHE cc_start: 0.7138 (t80) cc_final: 0.6721 (t80) REVERT: B 121 MET cc_start: 0.8097 (ttm) cc_final: 0.7854 (tpp) REVERT: B 318 MET cc_start: 0.5651 (mmm) cc_final: 0.5200 (tpt) REVERT: B 356 ASP cc_start: 0.8649 (m-30) cc_final: 0.8077 (t0) REVERT: B 373 ASP cc_start: 0.8191 (p0) cc_final: 0.7957 (t0) REVERT: B 499 ILE cc_start: 0.8176 (mt) cc_final: 0.7818 (tp) REVERT: B 520 MET cc_start: 0.7554 (tmm) cc_final: 0.7276 (tmm) REVERT: B 561 GLU cc_start: 0.7490 (pt0) cc_final: 0.7084 (pt0) REVERT: B 578 LEU cc_start: 0.8314 (mt) cc_final: 0.7850 (pp) REVERT: B 605 LEU cc_start: 0.8395 (tp) cc_final: 0.8021 (tp) REVERT: B 672 ASP cc_start: 0.8768 (t0) cc_final: 0.8460 (t0) REVERT: B 673 MET cc_start: 0.8474 (tpp) cc_final: 0.7858 (tpp) REVERT: B 688 MET cc_start: 0.8280 (ppp) cc_final: 0.8009 (ppp) REVERT: B 741 TRP cc_start: 0.8477 (t-100) cc_final: 0.7358 (t-100) REVERT: B 977 MET cc_start: 0.9099 (mmm) cc_final: 0.8547 (mmm) REVERT: B 1161 ASP cc_start: 0.8951 (p0) cc_final: 0.8673 (p0) REVERT: B 1172 GLU cc_start: 0.9028 (tt0) cc_final: 0.8224 (tm-30) REVERT: C 65 GLU cc_start: 0.7595 (mp0) cc_final: 0.7279 (mp0) REVERT: C 66 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8385 (p) REVERT: C 169 ASP cc_start: 0.6439 (m-30) cc_final: 0.5819 (m-30) REVERT: C 318 MET cc_start: 0.5595 (tpt) cc_final: 0.5217 (tpt) REVERT: C 384 ILE cc_start: 0.9503 (pt) cc_final: 0.9232 (mp) REVERT: C 456 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8681 (mmmm) REVERT: C 543 TYR cc_start: 0.7429 (p90) cc_final: 0.6689 (p90) REVERT: C 567 LYS cc_start: 0.8321 (tppt) cc_final: 0.8074 (tppt) REVERT: C 582 HIS cc_start: 0.7069 (t70) cc_final: 0.6791 (t70) REVERT: C 965 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8121 (mm) REVERT: C 968 MET cc_start: 0.8055 (tpt) cc_final: 0.7194 (pmm) REVERT: C 977 MET cc_start: 0.9190 (mmm) cc_final: 0.8862 (mmm) REVERT: C 988 ASP cc_start: 0.8799 (m-30) cc_final: 0.8412 (m-30) REVERT: C 1015 GLN cc_start: 0.8464 (tp40) cc_final: 0.7995 (tp40) REVERT: C 1109 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9013 (mm) REVERT: C 1149 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9286 (tp) REVERT: C 1161 ASP cc_start: 0.8880 (p0) cc_final: 0.8573 (p0) REVERT: C 1165 GLU cc_start: 0.9110 (tt0) cc_final: 0.8811 (tt0) REVERT: C 1217 LEU cc_start: 0.9567 (mm) cc_final: 0.9346 (mm) REVERT: C 1314 MET cc_start: 0.8795 (mpp) cc_final: 0.8169 (mpp) REVERT: D 74 PHE cc_start: 0.8420 (t80) cc_final: 0.8128 (t80) REVERT: D 183 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7284 (mp) REVERT: D 318 MET cc_start: 0.5562 (mmm) cc_final: 0.4912 (tpt) REVERT: D 356 ASP cc_start: 0.8662 (m-30) cc_final: 0.8080 (t0) REVERT: D 373 ASP cc_start: 0.8171 (p0) cc_final: 0.7966 (t0) REVERT: D 499 ILE cc_start: 0.8274 (mt) cc_final: 0.7882 (tp) REVERT: D 500 MET cc_start: 0.6668 (ttt) cc_final: 0.6455 (mtp) REVERT: D 520 MET cc_start: 0.7484 (tmm) cc_final: 0.7254 (tmm) REVERT: D 561 GLU cc_start: 0.7473 (pt0) cc_final: 0.7070 (pt0) REVERT: D 578 LEU cc_start: 0.8300 (mt) cc_final: 0.7840 (pp) REVERT: D 605 LEU cc_start: 0.8404 (tp) cc_final: 0.8055 (tp) REVERT: D 672 ASP cc_start: 0.8795 (t0) cc_final: 0.8453 (t0) REVERT: D 673 MET cc_start: 0.8407 (tpp) cc_final: 0.7941 (tpp) REVERT: D 688 MET cc_start: 0.8333 (ppp) cc_final: 0.8105 (ppp) REVERT: D 977 MET cc_start: 0.9114 (mmm) cc_final: 0.8521 (mmm) REVERT: D 1035 ASN cc_start: 0.7961 (m-40) cc_final: 0.7578 (m110) REVERT: D 1149 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9304 (tt) REVERT: D 1156 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8787 (mm) REVERT: D 1161 ASP cc_start: 0.8967 (p0) cc_final: 0.8656 (p0) REVERT: D 1217 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9166 (mm) REVERT: D 1237 TRP cc_start: 0.8001 (t60) cc_final: 0.7671 (t60) outliers start: 152 outliers final: 108 residues processed: 731 average time/residue: 0.2033 time to fit residues: 259.0865 Evaluate side-chains 667 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 548 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 SER 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 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 546 LEU 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 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 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 B residue 48 CYS Chi-restraints excluded: chain B residue 253 LEU 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 366 PHE Chi-restraints excluded: chain B residue 372 VAL 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 654 THR Chi-restraints excluded: chain B residue 675 LEU 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 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1110 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 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 SER 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 423 VAL Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 546 LEU 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 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 965 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1074 GLN 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 1298 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 183 LEU 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 366 PHE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 654 THR 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 1063 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1110 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 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: 10.0000 chunk 361 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 172 optimal weight: 0.0270 chunk 351 optimal weight: 5.9990 chunk 438 optimal weight: 10.0000 chunk 490 optimal weight: 9.9990 chunk 464 optimal weight: 6.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A1009 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 938 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C1009 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 HIS D 938 ASN ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.101608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080264 restraints weight = 117722.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.083150 restraints weight = 63104.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.085198 restraints weight = 41368.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086607 restraints weight = 30458.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.087543 restraints weight = 24378.879| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 41504 Z= 0.299 Angle : 0.892 15.917 56478 Z= 0.439 Chirality : 0.051 0.373 6514 Planarity : 0.006 0.073 7202 Dihedral : 5.670 30.246 5470 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.31 % Favored : 88.49 % Rotamer: Outliers : 4.00 % Allowed : 22.93 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.46 (0.11), residues: 5110 helix: 0.50 (0.17), residues: 872 sheet: -1.16 (0.12), residues: 1770 loop : -2.86 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 270 TYR 0.040 0.002 TYR D1007 PHE 0.028 0.003 PHE A 458 TRP 0.020 0.002 TRP C 765 HIS 0.010 0.002 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.30 (41420) covalent geometry : angle 0.88056 / 0.44 (56270) SS BOND : bond 0.00397 / 0.27 ( 44) SS BOND : angle 1.79874 / 1.16 ( 88) hydrogen bonds : bond 0.05618 / 3.78 ( 540) hydrogen bonds : angle 5.32233 / 3.60 ( 1620) link_BETA1-4 : bond 0.00297 / 0.19 ( 12) link_BETA1-4 : angle 2.42108 / 1.58 ( 36) link_NAG-ASN : bond 0.00824 / 0.56 ( 28) link_NAG-ASN : angle 3.10617 / 2.08 ( 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 738 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 559 time to evaluate : 1.601 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: 0.8993 (t) cc_final: 0.8670 (p) REVERT: A 199 PHE cc_start: 0.7955 (m-80) cc_final: 0.7667 (m-80) REVERT: A 384 ILE cc_start: 0.9546 (pt) cc_final: 0.9190 (mm) REVERT: A 456 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8967 (mmmm) REVERT: A 543 TYR cc_start: 0.7538 (p90) cc_final: 0.7295 (p90) REVERT: A 567 LYS cc_start: 0.8471 (tppt) cc_final: 0.8203 (tppt) REVERT: A 687 LYS cc_start: 0.9190 (tttt) cc_final: 0.8675 (tptt) REVERT: A 851 ASN cc_start: 0.9085 (m-40) cc_final: 0.8415 (m110) REVERT: A 968 MET cc_start: 0.8403 (tpp) cc_final: 0.7113 (pmm) REVERT: A 988 ASP cc_start: 0.8990 (m-30) cc_final: 0.8614 (m-30) REVERT: A 1109 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9130 (mm) REVERT: A 1149 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9467 (tt) REVERT: A 1161 ASP cc_start: 0.9023 (p0) cc_final: 0.8730 (p0) REVERT: A 1165 GLU cc_start: 0.9182 (tt0) cc_final: 0.8873 (tt0) REVERT: A 1314 MET cc_start: 0.8709 (mpp) cc_final: 0.8023 (mpp) REVERT: B 114 PHE cc_start: 0.7198 (t80) cc_final: 0.6706 (t80) REVERT: B 121 MET cc_start: 0.8190 (ttm) cc_final: 0.7989 (tpp) REVERT: B 169 ASP cc_start: 0.7015 (t0) cc_final: 0.6783 (t0) REVERT: B 318 MET cc_start: 0.6056 (mmm) cc_final: 0.5562 (tpt) REVERT: B 373 ASP cc_start: 0.8425 (p0) cc_final: 0.7991 (t0) REVERT: B 520 MET cc_start: 0.7641 (tmm) cc_final: 0.7327 (tmm) REVERT: B 561 GLU cc_start: 0.7556 (pt0) cc_final: 0.7129 (pt0) REVERT: B 578 LEU cc_start: 0.8454 (mt) cc_final: 0.7957 (pp) REVERT: B 605 LEU cc_start: 0.8408 (tp) cc_final: 0.7966 (tp) REVERT: B 627 LEU cc_start: 0.9325 (tp) cc_final: 0.9121 (tt) REVERT: B 669 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8579 (t80) REVERT: B 672 ASP cc_start: 0.8907 (t0) cc_final: 0.8623 (t0) REVERT: B 673 MET cc_start: 0.8742 (tpp) cc_final: 0.8386 (tpp) REVERT: B 688 MET cc_start: 0.8302 (ppp) cc_final: 0.8070 (ppp) REVERT: B 811 LYS cc_start: 0.8329 (mmtp) cc_final: 0.7933 (mmtm) REVERT: B 934 LYS cc_start: 0.8241 (tppt) cc_final: 0.7349 (mmmt) REVERT: B 977 MET cc_start: 0.9194 (mmm) cc_final: 0.8671 (mmm) REVERT: B 1147 LYS cc_start: 0.9124 (mttp) cc_final: 0.8603 (mttp) REVERT: B 1161 ASP cc_start: 0.9038 (p0) cc_final: 0.8781 (p0) REVERT: B 1172 GLU cc_start: 0.9106 (tt0) cc_final: 0.8178 (tm-30) REVERT: B 1311 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 65 GLU cc_start: 0.7705 (mp0) cc_final: 0.7412 (mp0) REVERT: C 66 SER cc_start: 0.9089 (t) cc_final: 0.8704 (p) REVERT: C 318 MET cc_start: 0.6090 (tpt) cc_final: 0.5695 (tpt) REVERT: C 384 ILE cc_start: 0.9593 (pt) cc_final: 0.9159 (mm) REVERT: C 456 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8974 (mmmm) REVERT: C 567 LYS cc_start: 0.8471 (tppt) cc_final: 0.8236 (tppt) REVERT: C 687 LYS cc_start: 0.9196 (tttt) cc_final: 0.8654 (tptt) REVERT: C 965 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8095 (mm) REVERT: C 1015 GLN cc_start: 0.8434 (tp40) cc_final: 0.8137 (tp40) REVERT: C 1109 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9115 (mm) REVERT: C 1149 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9428 (tt) REVERT: C 1161 ASP cc_start: 0.9005 (p0) cc_final: 0.8721 (p0) REVERT: C 1165 GLU cc_start: 0.9189 (tt0) cc_final: 0.8885 (tt0) REVERT: C 1217 LEU cc_start: 0.9644 (mm) cc_final: 0.9373 (mm) REVERT: C 1314 MET cc_start: 0.8706 (mpp) cc_final: 0.8046 (mpp) REVERT: D 74 PHE cc_start: 0.8519 (t80) cc_final: 0.8279 (t80) REVERT: D 318 MET cc_start: 0.6056 (mmm) cc_final: 0.5571 (tpt) REVERT: D 500 MET cc_start: 0.7271 (ttt) cc_final: 0.6970 (mtp) REVERT: D 520 MET cc_start: 0.7581 (tmm) cc_final: 0.7316 (tmm) REVERT: D 541 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6505 (pt) REVERT: D 561 GLU cc_start: 0.7542 (pt0) cc_final: 0.7156 (pt0) REVERT: D 578 LEU cc_start: 0.8454 (mt) cc_final: 0.7914 (pp) REVERT: D 605 LEU cc_start: 0.8429 (tp) cc_final: 0.7959 (tp) REVERT: D 672 ASP cc_start: 0.8897 (t0) cc_final: 0.8578 (t0) REVERT: D 673 MET cc_start: 0.8715 (tpp) cc_final: 0.8293 (tpp) REVERT: D 688 MET cc_start: 0.8317 (ppp) cc_final: 0.8076 (ppp) REVERT: D 770 PHE cc_start: 0.8394 (t80) cc_final: 0.8169 (t80) REVERT: D 811 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7898 (mmtm) REVERT: D 934 LYS cc_start: 0.8136 (tppt) cc_final: 0.7281 (mmmt) REVERT: D 961 ASN cc_start: 0.8672 (t0) cc_final: 0.8383 (t0) REVERT: D 1147 LYS cc_start: 0.9112 (mttp) cc_final: 0.8742 (mttp) REVERT: D 1149 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9456 (tt) REVERT: D 1311 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7703 (mp0) outliers start: 179 outliers final: 131 residues processed: 688 average time/residue: 0.2068 time to fit residues: 248.5632 Evaluate side-chains 665 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 524 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 104 THR 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 351 SER 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 514 LEU 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 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 1007 TYR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1087 LEU 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 A residue 1305 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 253 LEU 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 355 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 ARG 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 1080 PHE 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 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1311 GLU Chi-restraints excluded: chain B residue 1323 TYR Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 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 351 SER 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 546 LEU 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 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 965 LEU Chi-restraints excluded: chain C residue 1007 TYR Chi-restraints excluded: chain C residue 1035 ASN Chi-restraints excluded: chain C residue 1041 LEU 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 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 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1305 LEU Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain D residue 48 CYS 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 355 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR 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 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1128 LEU 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 1305 LEU Chi-restraints excluded: chain D residue 1311 GLU Chi-restraints excluded: chain D residue 1323 TYR 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: 8.9990 chunk 74 optimal weight: 20.0000 chunk 116 optimal weight: 0.0670 chunk 415 optimal weight: 9.9990 chunk 179 optimal weight: 0.0170 chunk 98 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 283 optimal weight: 8.9990 chunk 394 optimal weight: 0.1980 chunk 152 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 overall best weight: 2.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS C 851 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.103742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.082244 restraints weight = 117042.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085250 restraints weight = 62522.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.087363 restraints weight = 40660.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088772 restraints weight = 29788.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089758 restraints weight = 23888.693| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41504 Z= 0.197 Angle : 0.844 16.340 56478 Z= 0.407 Chirality : 0.050 0.445 6514 Planarity : 0.005 0.065 7202 Dihedral : 5.509 31.883 5470 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.51 % Favored : 90.29 % Rotamer: Outliers : 3.31 % Allowed : 24.61 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.11), residues: 5110 helix: 0.65 (0.17), residues: 866 sheet: -1.11 (0.12), residues: 1716 loop : -2.77 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 338 TYR 0.043 0.002 TYR D1007 PHE 0.035 0.002 PHE C 192 TRP 0.017 0.002 TRP C 436 HIS 0.007 0.001 HIS D 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (41420) covalent geometry : angle 0.83222 / 0.40 (56270) SS BOND : bond 0.00521 / 0.33 ( 44) SS BOND : angle 1.78133 / 1.24 ( 88) hydrogen bonds : bond 0.05253 / 3.53 ( 540) hydrogen bonds : angle 4.97270 / 3.38 ( 1620) link_BETA1-4 : bond 0.00421 / 0.25 ( 12) link_BETA1-4 : angle 2.37959 / 1.60 ( 36) link_NAG-ASN : bond 0.00703 / 0.49 ( 28) link_NAG-ASN : angle 3.02272 / 2.04 ( 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 715 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 567 time to evaluate : 1.634 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: 0.9010 (t) cc_final: 0.8686 (p) REVERT: A 199 PHE cc_start: 0.7943 (m-80) cc_final: 0.7662 (m-80) REVERT: A 246 MET cc_start: 0.6355 (mmt) cc_final: 0.5886 (mmt) REVERT: A 456 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8948 (mmmm) REVERT: A 567 LYS cc_start: 0.8430 (tppt) cc_final: 0.8204 (tppt) REVERT: A 665 ASP cc_start: 0.7937 (t0) cc_final: 0.7655 (t70) REVERT: A 687 LYS cc_start: 0.9212 (tttt) cc_final: 0.8660 (tptt) REVERT: A 851 ASN cc_start: 0.8996 (m-40) cc_final: 0.8319 (m110) REVERT: A 968 MET cc_start: 0.8358 (tpp) cc_final: 0.7221 (pmm) REVERT: A 988 ASP cc_start: 0.8979 (m-30) cc_final: 0.8582 (m-30) REVERT: A 1016 LEU cc_start: 0.9147 (mp) cc_final: 0.8919 (mp) REVERT: A 1109 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9093 (mm) REVERT: A 1121 VAL cc_start: 0.8954 (m) cc_final: 0.8733 (p) REVERT: A 1149 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9404 (tt) REVERT: A 1161 ASP cc_start: 0.8986 (p0) cc_final: 0.8685 (p0) REVERT: A 1165 GLU cc_start: 0.9178 (tt0) cc_final: 0.8878 (tt0) REVERT: A 1314 MET cc_start: 0.8792 (mpp) cc_final: 0.8068 (mpp) REVERT: B 32 MET cc_start: 0.7975 (ttp) cc_final: 0.7559 (ttp) REVERT: B 87 VAL cc_start: 0.8382 (p) cc_final: 0.8149 (t) REVERT: B 114 PHE cc_start: 0.6797 (t80) cc_final: 0.6573 (t80) REVERT: B 169 ASP cc_start: 0.6839 (t0) cc_final: 0.6597 (t0) REVERT: B 318 MET cc_start: 0.6069 (mmm) cc_final: 0.5577 (tpt) REVERT: B 373 ASP cc_start: 0.8331 (p0) cc_final: 0.7966 (t0) REVERT: B 500 MET cc_start: 0.7133 (ttt) cc_final: 0.6563 (ttm) REVERT: B 520 MET cc_start: 0.7680 (tmm) cc_final: 0.7401 (tmm) REVERT: B 550 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: B 561 GLU cc_start: 0.7471 (pt0) cc_final: 0.7124 (pt0) REVERT: B 578 LEU cc_start: 0.8460 (mt) cc_final: 0.8024 (pp) REVERT: B 602 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7014 (tm-30) REVERT: B 605 LEU cc_start: 0.8425 (tp) cc_final: 0.8212 (tp) REVERT: B 627 LEU cc_start: 0.9323 (tp) cc_final: 0.9108 (tt) REVERT: B 672 ASP cc_start: 0.8889 (t0) cc_final: 0.8684 (t0) REVERT: B 673 MET cc_start: 0.8849 (tpp) cc_final: 0.8097 (tpp) REVERT: B 688 MET cc_start: 0.8331 (ppp) cc_final: 0.8106 (ppp) REVERT: B 811 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7889 (mmtm) REVERT: B 934 LYS cc_start: 0.8185 (tppt) cc_final: 0.7373 (mmmt) REVERT: B 977 MET cc_start: 0.9207 (mmm) cc_final: 0.8697 (mmm) REVERT: B 1147 LYS cc_start: 0.9115 (mttp) cc_final: 0.8561 (mttp) REVERT: B 1161 ASP cc_start: 0.9000 (p0) cc_final: 0.8784 (p0) REVERT: B 1172 GLU cc_start: 0.9088 (tt0) cc_final: 0.8170 (tm-30) REVERT: B 1311 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: C 66 SER cc_start: 0.9001 (t) cc_final: 0.8651 (p) REVERT: C 246 MET cc_start: 0.6203 (mmt) cc_final: 0.6001 (mmt) REVERT: C 384 ILE cc_start: 0.9562 (pt) cc_final: 0.9326 (mp) REVERT: C 456 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8945 (mmmm) REVERT: C 567 LYS cc_start: 0.8440 (tppt) cc_final: 0.8213 (tppt) REVERT: C 687 LYS cc_start: 0.9216 (tttt) cc_final: 0.8605 (tptt) REVERT: C 851 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8353 (m-40) REVERT: C 968 MET cc_start: 0.8216 (tpp) cc_final: 0.6808 (pmm) REVERT: C 988 ASP cc_start: 0.8916 (m-30) cc_final: 0.8520 (m-30) REVERT: C 1015 GLN cc_start: 0.8410 (tp40) cc_final: 0.8148 (tp40) REVERT: C 1018 TYR cc_start: 0.8207 (m-80) cc_final: 0.7804 (t80) REVERT: C 1109 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9101 (mm) REVERT: C 1121 VAL cc_start: 0.8946 (m) cc_final: 0.8726 (p) REVERT: C 1149 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9391 (tt) REVERT: C 1161 ASP cc_start: 0.8962 (p0) cc_final: 0.8682 (p0) REVERT: C 1165 GLU cc_start: 0.9175 (tt0) cc_final: 0.8867 (tt0) REVERT: C 1217 LEU cc_start: 0.9603 (mm) cc_final: 0.9389 (mm) REVERT: C 1314 MET cc_start: 0.8736 (mpp) cc_final: 0.8022 (mpp) REVERT: D 74 PHE cc_start: 0.8455 (t80) cc_final: 0.8222 (t80) REVERT: D 318 MET cc_start: 0.6061 (mmm) cc_final: 0.5575 (tpt) REVERT: D 356 ASP cc_start: 0.8642 (m-30) cc_final: 0.7607 (t0) REVERT: D 373 ASP cc_start: 0.8612 (p0) cc_final: 0.8085 (t70) REVERT: D 520 MET cc_start: 0.7581 (tmm) cc_final: 0.7351 (tmm) REVERT: D 541 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6384 (pt) REVERT: D 561 GLU cc_start: 0.7488 (pt0) cc_final: 0.7132 (pt0) REVERT: D 602 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7036 (tm-30) REVERT: D 605 LEU cc_start: 0.8427 (tp) cc_final: 0.8210 (tp) REVERT: D 672 ASP cc_start: 0.8890 (t0) cc_final: 0.8561 (t0) REVERT: D 673 MET cc_start: 0.8685 (tpp) cc_final: 0.8278 (tpp) REVERT: D 688 MET cc_start: 0.8349 (ppp) cc_final: 0.8117 (ppp) REVERT: D 770 PHE cc_start: 0.8350 (t80) cc_final: 0.8144 (t80) REVERT: D 811 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7851 (mmtm) REVERT: D 934 LYS cc_start: 0.8207 (tppt) cc_final: 0.7336 (mmmt) REVERT: D 961 ASN cc_start: 0.8739 (t0) cc_final: 0.8455 (t0) REVERT: D 977 MET cc_start: 0.9164 (mmm) cc_final: 0.8537 (mmm) REVERT: D 1147 LYS cc_start: 0.9085 (mttp) cc_final: 0.8575 (mttp) REVERT: D 1149 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9375 (tt) REVERT: D 1311 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7710 (mp0) outliers start: 148 outliers final: 118 residues processed: 679 average time/residue: 0.2062 time to fit residues: 243.8977 Evaluate side-chains 669 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 541 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU 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 346 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 353 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 656 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 1007 TYR Chi-restraints excluded: chain A residue 1055 TYR 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 253 LEU 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 355 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 645 ARG 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 1080 PHE 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 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1311 GLU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 51 LEU 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 351 SER Chi-restraints excluded: chain C residue 353 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 546 LEU 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 675 LEU Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 798 MET Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 851 ASN Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1007 TYR 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 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 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS 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 355 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 550 ASP Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR 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 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1128 LEU 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 1305 LEU Chi-restraints excluded: chain D residue 1311 GLU 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: 6.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 425 optimal weight: 6.9990 chunk 332 optimal weight: 0.4980 chunk 91 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 432 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS C 851 ASN ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** 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 = 0.3887 r_free = 0.3887 target = 0.103840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082249 restraints weight = 117179.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.085266 restraints weight = 62959.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.087334 restraints weight = 41023.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.088719 restraints weight = 30229.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.089732 restraints weight = 24357.503| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41504 Z= 0.195 Angle : 0.847 16.472 56478 Z= 0.407 Chirality : 0.051 0.452 6514 Planarity : 0.005 0.066 7202 Dihedral : 5.506 32.433 5470 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.72 % Favored : 89.08 % Rotamer: Outliers : 3.15 % Allowed : 24.81 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.34 (0.11), residues: 5110 helix: 0.65 (0.17), residues: 878 sheet: -1.14 (0.12), residues: 1712 loop : -2.74 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 338 TYR 0.033 0.002 TYR C1012 PHE 0.038 0.002 PHE C 192 TRP 0.019 0.002 TRP C 436 HIS 0.006 0.001 HIS B 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (41420) covalent geometry : angle 0.83557 / 0.40 (56270) SS BOND : bond 0.00327 / 0.22 ( 44) SS BOND : angle 1.69276 / 1.16 ( 88) hydrogen bonds : bond 0.05298 / 3.55 ( 540) hydrogen bonds : angle 4.92468 / 3.35 ( 1620) link_BETA1-4 : bond 0.00412 / 0.26 ( 12) link_BETA1-4 : angle 2.38589 / 1.61 ( 36) link_NAG-ASN : bond 0.00696 / 0.48 ( 28) link_NAG-ASN : angle 2.98399 / 2.01 ( 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 708 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 567 time to evaluate : 1.132 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 199 PHE cc_start: 0.7847 (m-80) cc_final: 0.7586 (m-80) REVERT: A 246 MET cc_start: 0.6417 (mmt) cc_final: 0.6002 (mmt) REVERT: A 456 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8952 (mmmm) REVERT: A 520 MET cc_start: 0.7744 (tmm) cc_final: 0.7477 (tmm) REVERT: A 665 ASP cc_start: 0.7902 (t0) cc_final: 0.7614 (t70) REVERT: A 687 LYS cc_start: 0.9221 (tttt) cc_final: 0.8657 (tptt) REVERT: A 851 ASN cc_start: 0.8990 (m-40) cc_final: 0.8340 (m110) REVERT: A 988 ASP cc_start: 0.8958 (m-30) cc_final: 0.8561 (m-30) REVERT: A 1016 LEU cc_start: 0.9164 (mp) cc_final: 0.8915 (mp) REVERT: A 1109 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9064 (mm) REVERT: A 1121 VAL cc_start: 0.8956 (m) cc_final: 0.8740 (p) REVERT: A 1149 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9409 (tt) REVERT: A 1161 ASP cc_start: 0.8968 (p0) cc_final: 0.8660 (p0) REVERT: A 1165 GLU cc_start: 0.9182 (tt0) cc_final: 0.8923 (tt0) REVERT: A 1314 MET cc_start: 0.8760 (mpp) cc_final: 0.8066 (mpp) REVERT: B 169 ASP cc_start: 0.6798 (t0) cc_final: 0.6565 (t0) REVERT: B 318 MET cc_start: 0.6091 (mmm) cc_final: 0.5594 (tpt) REVERT: B 356 ASP cc_start: 0.8688 (m-30) cc_final: 0.8393 (m-30) REVERT: B 373 ASP cc_start: 0.8311 (p0) cc_final: 0.7981 (t0) REVERT: B 500 MET cc_start: 0.7222 (ttt) cc_final: 0.6808 (ttm) REVERT: B 520 MET cc_start: 0.7674 (tmm) cc_final: 0.7406 (tmm) REVERT: B 550 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: B 554 ASP cc_start: 0.6223 (t0) cc_final: 0.5921 (t0) REVERT: B 561 GLU cc_start: 0.7487 (pt0) cc_final: 0.7144 (pt0) REVERT: B 602 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B 605 LEU cc_start: 0.8306 (tp) cc_final: 0.8075 (tp) REVERT: B 627 LEU cc_start: 0.9330 (tp) cc_final: 0.9113 (tt) REVERT: B 669 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8604 (t80) REVERT: B 672 ASP cc_start: 0.8879 (t0) cc_final: 0.8636 (t0) REVERT: B 673 MET cc_start: 0.8840 (tpp) cc_final: 0.8287 (tpp) REVERT: B 688 MET cc_start: 0.8330 (ppp) cc_final: 0.8114 (ppp) REVERT: B 811 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7870 (mmtp) REVERT: B 934 LYS cc_start: 0.8134 (tppt) cc_final: 0.7301 (mmmt) REVERT: B 977 MET cc_start: 0.9174 (mmm) cc_final: 0.8669 (mmm) REVERT: B 1147 LYS cc_start: 0.9103 (mttp) cc_final: 0.8544 (mttp) REVERT: B 1172 GLU cc_start: 0.9087 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 1311 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: C 246 MET cc_start: 0.6325 (mmt) cc_final: 0.5797 (mmt) REVERT: C 384 ILE cc_start: 0.9542 (pt) cc_final: 0.9306 (mp) REVERT: C 456 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8946 (mmmm) REVERT: C 665 ASP cc_start: 0.7926 (t0) cc_final: 0.7685 (t0) REVERT: C 687 LYS cc_start: 0.9230 (tttt) cc_final: 0.8613 (tptt) REVERT: C 851 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8487 (m-40) REVERT: C 968 MET cc_start: 0.8375 (tpp) cc_final: 0.7231 (pmm) REVERT: C 988 ASP cc_start: 0.8902 (m-30) cc_final: 0.8447 (m-30) REVERT: C 1015 GLN cc_start: 0.8432 (tp40) cc_final: 0.8132 (tp40) REVERT: C 1018 TYR cc_start: 0.8166 (m-80) cc_final: 0.7878 (t80) REVERT: C 1074 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8312 (tp-100) REVERT: C 1109 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9089 (mm) REVERT: C 1121 VAL cc_start: 0.8949 (m) cc_final: 0.8737 (p) REVERT: C 1149 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9379 (tt) REVERT: C 1161 ASP cc_start: 0.8952 (p0) cc_final: 0.8682 (p0) REVERT: C 1165 GLU cc_start: 0.9167 (tt0) cc_final: 0.8860 (tt0) REVERT: C 1217 LEU cc_start: 0.9591 (mm) cc_final: 0.9372 (mm) REVERT: C 1314 MET cc_start: 0.8733 (mpp) cc_final: 0.8041 (mpp) REVERT: D 74 PHE cc_start: 0.8457 (t80) cc_final: 0.8235 (t80) REVERT: D 318 MET cc_start: 0.6101 (mmm) cc_final: 0.5605 (tpt) REVERT: D 373 ASP cc_start: 0.8571 (p0) cc_final: 0.8066 (t70) REVERT: D 500 MET cc_start: 0.7557 (mtp) cc_final: 0.6906 (mtp) REVERT: D 520 MET cc_start: 0.7672 (tmm) cc_final: 0.7444 (tmm) REVERT: D 541 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6433 (pt) REVERT: D 550 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6394 (m-30) REVERT: D 561 GLU cc_start: 0.7475 (pt0) cc_final: 0.7142 (pt0) REVERT: D 673 MET cc_start: 0.8757 (tpp) cc_final: 0.8243 (tpp) REVERT: D 688 MET cc_start: 0.8337 (ppp) cc_final: 0.8120 (ppp) REVERT: D 811 LYS cc_start: 0.8278 (mmtp) cc_final: 0.7830 (mmtm) REVERT: D 934 LYS cc_start: 0.8102 (tppt) cc_final: 0.7343 (mmmt) REVERT: D 961 ASN cc_start: 0.8740 (t0) cc_final: 0.8461 (t0) REVERT: D 977 MET cc_start: 0.9153 (mmm) cc_final: 0.8580 (mmm) REVERT: D 1147 LYS cc_start: 0.9065 (mttp) cc_final: 0.8548 (mttp) REVERT: D 1149 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9357 (tt) outliers start: 141 outliers final: 117 residues processed: 670 average time/residue: 0.2042 time to fit residues: 237.8544 Evaluate side-chains 670 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 541 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 346 THR 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 656 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 1007 TYR Chi-restraints excluded: chain A residue 1055 TYR 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 253 LEU 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 355 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 645 ARG 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 949 SER Chi-restraints excluded: chain B residue 1080 PHE 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 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1311 GLU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 51 LEU 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 351 SER 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 605 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 675 LEU Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 798 MET Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 851 ASN Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1007 TYR 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 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 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 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 355 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 645 ARG 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 1080 PHE Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1128 LEU 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 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 500 optimal weight: 0.9980 chunk 480 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 395 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C1179 ASN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.083709 restraints weight = 117781.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.086727 restraints weight = 62916.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.088848 restraints weight = 41006.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.090324 restraints weight = 30026.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091210 restraints weight = 24063.489| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41504 Z= 0.160 Angle : 0.832 16.244 56478 Z= 0.397 Chirality : 0.050 0.437 6514 Planarity : 0.005 0.059 7202 Dihedral : 5.337 31.773 5470 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.22 % Favored : 90.61 % Rotamer: Outliers : 2.93 % Allowed : 25.21 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.24 (0.12), residues: 5110 helix: 0.77 (0.17), residues: 874 sheet: -1.12 (0.12), residues: 1722 loop : -2.64 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.030 0.002 TYR C 800 PHE 0.066 0.002 PHE B 114 TRP 0.016 0.001 TRP C 436 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (41420) covalent geometry : angle 0.82116 / 0.39 (56270) SS BOND : bond 0.00256 / 0.18 ( 44) SS BOND : angle 1.58278 / 1.10 ( 88) hydrogen bonds : bond 0.05041 / 3.37 ( 540) hydrogen bonds : angle 4.72436 / 3.23 ( 1620) link_BETA1-4 : bond 0.00457 / 0.28 ( 12) link_BETA1-4 : angle 2.35140 / 1.60 ( 36) link_NAG-ASN : bond 0.00657 / 0.45 ( 28) link_NAG-ASN : angle 2.93518 / 1.98 ( 84) =============================================================================== Job complete usr+sys time: 7558.27 seconds wall clock time: 132 minutes 1.67 seconds (7921.67 seconds total)